| Transcript | Gene symbol | Prediction | Tree vote | Model | Prediction problem | Splice site change | Known ClinVar disease mutation | Potential ClinVar disease mutation | Amino acid changes | Variant type | dbSNP ID | Protein length | Features at a glance |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ENST00000510168(MANE Select) | ATP2C1 | Deleterious | 71|29 | simple_ | No | Single base exchange | Normal |
| |||||
| ATP2C1 | Deleterious | 72|28 | simple_ | No | Single base exchange | Normal |
| ||||||
| ATP2C1 | Deleterious | 73|27 | simple_ | No | Single base exchange | Normal |
| ||||||
| ATP2C1 | Deleterious | 75|25 | simple_ | No | Single base exchange | Normal |
| ||||||
| ATP2C1 | Deleterious | 76|24 | simple_ | No | Single base exchange | Normal |
| ||||||
| ATP2C1 | Deleterious | 76|24 | simple_ | No | Single base exchange | Normal |
| ||||||
| ATP2C1 | Deleterious | 76|24 | simple_ | No | Single base exchange | Normal |
| ||||||
| ATP2C1 | Deleterious | 77|23 | simple_ | No | Single base exchange | Normal |
| ||||||
| ATP2C1 | Deleterious | 77|23 | simple_ | No | Single base exchange | Normal |
| ||||||
| ATP2C1 | Deleterious | 80|20 | simple_ | No | Single base exchange | Normal |
| ||||||
| ATP2C1 | Deleterious | 80|20 | simple_ | No | Single base exchange | Normal |
| ||||||
| ATP2C1 | Deleterious | 80|20 | simple_ | No | Single base exchange | Normal |
|
| Analysed issue | Analysis result | ||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Variant | Chr3:130996075A>G (GRCh38) | ||||||||||||||||
| Gene symbol | ATP2C1 | ||||||||||||||||
| Gene constraints | LOEUF: 0.40, LOF (oe): 0.28, misssense (oe): 0.65, synonymous (oe): 0.89 (gnomAD) | ||||||||||||||||
| Ensembl transcript ID | ENST00000510168.6 | ||||||||||||||||
| Genbank transcript ID | NM_001378687 (exact from MANE) | ||||||||||||||||
| UniProt / AlphaMissense peptide | AT2C1_HUMAN | AlphaMissense: transcript, gene | ||||||||||||||||
| Variant type | Single base exchange | ||||||||||||||||
| Gene region | CDS | ||||||||||||||||
| DNA changes | c.2090A>G g.145481A>G | ||||||||||||||||
| AA changes |
| ||||||||||||||||
| Frameshift | No | ||||||||||||||||
| Length of protein | Normal | ||||||||||||||||
| Pathogenic variant (ClinVar) | Variant not listed in ClinVar as (likely) pathogenic. | ||||||||||||||||
| Variant DBs |
| ||||||||||||||||
| Protein conservation | |||||||||||||||||
| Protein features |
| ||||||||||||||||
| Phylogenetic conservation |
| ||||||||||||||||
| Splice sites | No abrogation of potential splice sites predicted by MaxEntScan. | ||||||||||||||||
| Distance from splice site | N/A | ||||||||||||||||
| Kozak consensus sequence altered? | No | ||||||||||||||||
| poly(A) signal | N/A | ||||||||||||||||
| AA sequence altered | Yes | ||||||||||||||||
| Chromosome | 3 | ||||||||||||||||
| Strand | 1 | ||||||||||||||||
| Original gDNA sequence snippet | AGAGGGTAAAGGGATTTATAATAACATTAAAAATTTCGTTA | ||||||||||||||||
| Altered gDNA sequence snippet | AGAGGGTAAAGGGATTTATAGTAACATTAAAAATTTCGTTA | ||||||||||||||||
| Original cDNA sequence snippet | AGAGGGTAAAGGGATTTATAATAACATTAAAAATTTCGTTA | ||||||||||||||||
| Altered cDNA sequence snippet | AGAGGGTAAAGGGATTTATAGTAACATTAAAAATTTCGTTA | ||||||||||||||||
| Wildtype AA sequence | MKVARFQKIP NGENETMIPV LTSKKASELP VSEVASILQA DLQNGLNKCE VSHRRAFHGW NEFDISEDEP LWKKYISQFK NPLIMLLLAS AVISVLMHQF DDAVSITVAI LIVVTVAFVQ EYRSEKSLEE LSKLVPPECH CVREGKLEHT LARDLVPGDT VCLSVGDRVP ADLRLFEAVD LSIDESSLTG ETTPCSKVTA PQPAATNGDL ASRSNIAFMG TLVRCGKAKG VVIGTGENSE FGEVFKMMQA EEAPKTPLQK SMDLLGKQLS FYSFGIIGII MLVGWLLGKD ILEMFTISVS LAVAAIPEGL PIVVTVTLAL GVMRMVKKRA IVKKLPIVET LGCCNVICSD KTGTLTKNEM TVTHIFTSDG LHAEVTGVGY NQFGEVIVDG DVVHGFYNPA VSRIVEAGCV CNDAVIRNNT LMGKPTEGAL IALAMKMGLD GLQQDYIRKA EYPFSSEQKW MAVKCVHRTQ QDRPEICFMK GAYEQVIKYC TTYQSKGQTL TLTQQQRDVY QQEKARMGSA GLRVLALASG PELGQLTFLG LVGIIDPPRT GVKEAVTTLI ASGVSIKMIT GDSQETAVAI ASRLGLYSKT SQSVSGEEID AMDVQQLSQI VPKVAVFYRA SPRHKMKIIK SLQKNGSVVA MTGDGVNDAV ALKAADIGVA MGQTGTDVCK EAADMILVDD DFQTIMSAIE EGKGIYNNIK NFVRFQLSTS IAALTLISLA TLMNFPNPLN AMQILWINII MDGPPAQSLG VEPVDKDVIR KPPRNWKDSI LTKNLILKIL VSSIIIVCGT LFVFWRELRD NVITPRDTTM TFTCFVFFDM FNALSSRSQT KSVFEIGLCS NRMFCYAVLG SIMGQLLVIY FPPLQKVFQT ESLSILDLLF LLGLTSSVCI VAEIIKKVER SREKIQKHVS STSSSFLEV* | ||||||||||||||||
| Mutated AA sequence | MKVARFQKIP NGENETMIPV LTSKKASELP VSEVASILQA DLQNGLNKCE VSHRRAFHGW NEFDISEDEP LWKKYISQFK NPLIMLLLAS AVISVLMHQF DDAVSITVAI LIVVTVAFVQ EYRSEKSLEE LSKLVPPECH CVREGKLEHT LARDLVPGDT VCLSVGDRVP ADLRLFEAVD LSIDESSLTG ETTPCSKVTA PQPAATNGDL ASRSNIAFMG TLVRCGKAKG VVIGTGENSE FGEVFKMMQA EEAPKTPLQK SMDLLGKQLS FYSFGIIGII MLVGWLLGKD ILEMFTISVS LAVAAIPEGL PIVVTVTLAL GVMRMVKKRA IVKKLPIVET LGCCNVICSD KTGTLTKNEM TVTHIFTSDG LHAEVTGVGY NQFGEVIVDG DVVHGFYNPA VSRIVEAGCV CNDAVIRNNT LMGKPTEGAL IALAMKMGLD GLQQDYIRKA EYPFSSEQKW MAVKCVHRTQ QDRPEICFMK GAYEQVIKYC TTYQSKGQTL TLTQQQRDVY QQEKARMGSA GLRVLALASG PELGQLTFLG LVGIIDPPRT GVKEAVTTLI ASGVSIKMIT GDSQETAVAI ASRLGLYSKT SQSVSGEEID AMDVQQLSQI VPKVAVFYRA SPRHKMKIIK SLQKNGSVVA MTGDGVNDAV ALKAADIGVA MGQTGTDVCK EAADMILVDD DFQTIMSAIE EGKGIYSNIK NFVRFQLSTS IAALTLISLA TLMNFPNPLN AMQILWINII MDGPPAQSLG VEPVDKDVIR KPPRNWKDSI LTKNLILKIL VSSIIIVCGT LFVFWRELRD NVITPRDTTM TFTCFVFFDM FNALSSRSQT KSVFEIGLCS NRMFCYAVLG SIMGQLLVIY FPPLQKVFQT ESLSILDLLF LLGLTSSVCI VAEIIKKVER SREKIQKHVS STSSSFLEV* | ||||||||||||||||
| Position of stopcodon in wt / mu CDS | 2760 / 2760 | ||||||||||||||||
| Position (AA) of stopcodon in wt / mu AA sequence | 920 / 920 | ||||||||||||||||
| Position of stopcodon in wt / mu cDNA | 3194 / 3194 | ||||||||||||||||
| Position of start ATG in wt / mu cDNA | 435 / 435 | ||||||||||||||||
| Last intron/exon boundary | 3063 | ||||||||||||||||
| Theoretical NMD boundary in CDS | 2578 | ||||||||||||||||
| Length of CDS | 2760 | ||||||||||||||||
| Coding sequence (CDS) position | 2090 | ||||||||||||||||
| cDNA position | 2524 | ||||||||||||||||
| gDNA position | 145481 | ||||||||||||||||
| Chromosomal position | 130996075 | ||||||||||||||||
| Speed | 0.03 s | ||||||||||||||||
All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
| Analysed issue | Analysis result | ||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Variant | Chr3:130996075A>G (GRCh38) | ||||||||||||||||
| Gene symbol | ATP2C1 | ||||||||||||||||
| Gene constraints | LOEUF: 0.43, LOF (oe): 0.31, misssense (oe): 0.66, synonymous (oe): 0.89 (gnomAD) | ||||||||||||||||
| Ensembl transcript ID | ENST00000422190.6 | ||||||||||||||||
| Genbank transcript ID | NM_001001487 (by similarity), NM_001378513 (by similarity) | ||||||||||||||||
| UniProt / AlphaMissense peptide | AT2C1_HUMAN | AlphaMissense: transcript, gene | ||||||||||||||||
| Variant type | Single base exchange | ||||||||||||||||
| Gene region | CDS | ||||||||||||||||
| DNA changes | c.2090A>G g.145481A>G | ||||||||||||||||
| AA changes |
| ||||||||||||||||
| Frameshift | No | ||||||||||||||||
| Length of protein | Normal | ||||||||||||||||
| Pathogenic variant (ClinVar) | Variant not listed in ClinVar as (likely) pathogenic. | ||||||||||||||||
| Variant DBs |
| ||||||||||||||||
| Protein conservation | |||||||||||||||||
| Protein features |
| ||||||||||||||||
| Phylogenetic conservation |
| ||||||||||||||||
| Splice sites | No abrogation of potential splice sites predicted by MaxEntScan. | ||||||||||||||||
| Distance from splice site | N/A | ||||||||||||||||
| Kozak consensus sequence altered? | No | ||||||||||||||||
| poly(A) signal | N/A | ||||||||||||||||
| AA sequence altered | Yes | ||||||||||||||||
| Chromosome | 3 | ||||||||||||||||
| Strand | 1 | ||||||||||||||||
| Original gDNA sequence snippet | AGAGGGTAAAGGGATTTATAATAACATTAAAAATTTCGTTA | ||||||||||||||||
| Altered gDNA sequence snippet | AGAGGGTAAAGGGATTTATAGTAACATTAAAAATTTCGTTA | ||||||||||||||||
| Original cDNA sequence snippet | AGAGGGTAAAGGGATTTATAATAACATTAAAAATTTCGTTA | ||||||||||||||||
| Altered cDNA sequence snippet | AGAGGGTAAAGGGATTTATAGTAACATTAAAAATTTCGTTA | ||||||||||||||||
| Wildtype AA sequence | MKVARFQKIP NGENETMIPV LTSKKASELP VSEVASILQA DLQNGLNKCE VSHRRAFHGW NEFDISEDEP LWKKYISQFK NPLIMLLLAS AVISVLMHQF DDAVSITVAI LIVVTVAFVQ EYRSEKSLEE LSKLVPPECH CVREGKLEHT LARDLVPGDT VCLSVGDRVP ADLRLFEAVD LSIDESSLTG ETTPCSKVTA PQPAATNGDL ASRSNIAFMG TLVRCGKAKG VVIGTGENSE FGEVFKMMQA EEAPKTPLQK SMDLLGKQLS FYSFGIIGII MLVGWLLGKD ILEMFTISVS LAVAAIPEGL PIVVTVTLAL GVMRMVKKRA IVKKLPIVET LGCCNVICSD KTGTLTKNEM TVTHIFTSDG LHAEVTGVGY NQFGEVIVDG DVVHGFYNPA VSRIVEAGCV CNDAVIRNNT LMGKPTEGAL IALAMKMGLD GLQQDYIRKA EYPFSSEQKW MAVKCVHRTQ QDRPEICFMK GAYEQVIKYC TTYQSKGQTL TLTQQQRDVY QQEKARMGSA GLRVLALASG PELGQLTFLG LVGIIDPPRT GVKEAVTTLI ASGVSIKMIT GDSQETAVAI ASRLGLYSKT SQSVSGEEID AMDVQQLSQI VPKVAVFYRA SPRHKMKIIK SLQKNGSVVA MTGDGVNDAV ALKAADIGVA MGQTGTDVCK EAADMILVDD DFQTIMSAIE EGKGIYNNIK NFVRFQLSTS IAALTLISLA TLMNFPNPLN AMQILWINII MDGPPAQSLG VEPVDKDVIR KPPRNWKDSI LTKNLILKIL VSSIIIVCGT LFVFWRELRD NVITPRDTTM TFTCFVFFDM FNALSSRSQT KSVFEIGLCS NRMFCYAVLG SIMGQLLVIY FPPLQKVFQT ESLSILDLLF LLGLTSSVCI VAEIIKKVER SREKIQKHVW LWERSGQQLV EIHPHLETGL PLTEDVSCV* | ||||||||||||||||
| Mutated AA sequence | MKVARFQKIP NGENETMIPV LTSKKASELP VSEVASILQA DLQNGLNKCE VSHRRAFHGW NEFDISEDEP LWKKYISQFK NPLIMLLLAS AVISVLMHQF DDAVSITVAI LIVVTVAFVQ EYRSEKSLEE LSKLVPPECH CVREGKLEHT LARDLVPGDT VCLSVGDRVP ADLRLFEAVD LSIDESSLTG ETTPCSKVTA PQPAATNGDL ASRSNIAFMG TLVRCGKAKG VVIGTGENSE FGEVFKMMQA EEAPKTPLQK SMDLLGKQLS FYSFGIIGII MLVGWLLGKD ILEMFTISVS LAVAAIPEGL PIVVTVTLAL GVMRMVKKRA IVKKLPIVET LGCCNVICSD KTGTLTKNEM TVTHIFTSDG LHAEVTGVGY NQFGEVIVDG DVVHGFYNPA VSRIVEAGCV CNDAVIRNNT LMGKPTEGAL IALAMKMGLD GLQQDYIRKA EYPFSSEQKW MAVKCVHRTQ QDRPEICFMK GAYEQVIKYC TTYQSKGQTL TLTQQQRDVY QQEKARMGSA GLRVLALASG PELGQLTFLG LVGIIDPPRT GVKEAVTTLI ASGVSIKMIT GDSQETAVAI ASRLGLYSKT SQSVSGEEID AMDVQQLSQI VPKVAVFYRA SPRHKMKIIK SLQKNGSVVA MTGDGVNDAV ALKAADIGVA MGQTGTDVCK EAADMILVDD DFQTIMSAIE EGKGIYSNIK NFVRFQLSTS IAALTLISLA TLMNFPNPLN AMQILWINII MDGPPAQSLG VEPVDKDVIR KPPRNWKDSI LTKNLILKIL VSSIIIVCGT LFVFWRELRD NVITPRDTTM TFTCFVFFDM FNALSSRSQT KSVFEIGLCS NRMFCYAVLG SIMGQLLVIY FPPLQKVFQT ESLSILDLLF LLGLTSSVCI VAEIIKKVER SREKIQKHVW LWERSGQQLV EIHPHLETGL PLTEDVSCV* | ||||||||||||||||
| Position of stopcodon in wt / mu CDS | 2820 / 2820 | ||||||||||||||||
| Position (AA) of stopcodon in wt / mu AA sequence | 940 / 940 | ||||||||||||||||
| Position of stopcodon in wt / mu cDNA | 2949 / 2949 | ||||||||||||||||
| Position of start ATG in wt / mu cDNA | 130 / 130 | ||||||||||||||||
| Last intron/exon boundary | 2853 | ||||||||||||||||
| Theoretical NMD boundary in CDS | 2673 | ||||||||||||||||
| Length of CDS | 2820 | ||||||||||||||||
| Coding sequence (CDS) position | 2090 | ||||||||||||||||
| cDNA position | 2219 | ||||||||||||||||
| gDNA position | 145481 | ||||||||||||||||
| Chromosomal position | 130996075 | ||||||||||||||||
| Speed | 0.04 s | ||||||||||||||||
All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
| Analysed issue | Analysis result | ||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Variant | Chr3:130996075A>G (GRCh38) | ||||||||||||||||
| Gene symbol | ATP2C1 | ||||||||||||||||
| Gene constraints | LOEUF: 0.43, LOF (oe): 0.31, misssense (oe): 0.65, synonymous (oe): 0.88 (gnomAD) | ||||||||||||||||
| Ensembl transcript ID | ENST00000513801.5 | ||||||||||||||||
| Genbank transcript ID | NM_001378514 (by similarity), NM_001199183 (by similarity) | ||||||||||||||||
| UniProt / AlphaMissense peptide | AT2C1_HUMAN | AlphaMissense: transcript, gene | ||||||||||||||||
| Variant type | Single base exchange | ||||||||||||||||
| Gene region | CDS | ||||||||||||||||
| DNA changes | c.2042A>G g.145481A>G | ||||||||||||||||
| AA changes |
| ||||||||||||||||
| Frameshift | No | ||||||||||||||||
| Length of protein | Normal | ||||||||||||||||
| Pathogenic variant (ClinVar) | Variant not listed in ClinVar as (likely) pathogenic. | ||||||||||||||||
| Variant DBs |
| ||||||||||||||||
| Protein conservation | |||||||||||||||||
| Protein features |
| ||||||||||||||||
| Phylogenetic conservation |
| ||||||||||||||||
| Splice sites | No abrogation of potential splice sites predicted by MaxEntScan. | ||||||||||||||||
| Distance from splice site | N/A | ||||||||||||||||
| Kozak consensus sequence altered? | No | ||||||||||||||||
| poly(A) signal | N/A | ||||||||||||||||
| AA sequence altered | Yes | ||||||||||||||||
| Chromosome | 3 | ||||||||||||||||
| Strand | 1 | ||||||||||||||||
| Original gDNA sequence snippet | AGAGGGTAAAGGGATTTATAATAACATTAAAAATTTCGTTA | ||||||||||||||||
| Altered gDNA sequence snippet | AGAGGGTAAAGGGATTTATAGTAACATTAAAAATTTCGTTA | ||||||||||||||||
| Original cDNA sequence snippet | AGAGGGTAAAGGGATTTATAATAACATTAAAAATTTCGTTA | ||||||||||||||||
| Altered cDNA sequence snippet | AGAGGGTAAAGGGATTTATAGTAACATTAAAAATTTCGTTA | ||||||||||||||||
| Wildtype AA sequence | MIPVLTSKKA SELPVSEVAS ILQADLQNGL NKCEVSHRRA FHGWNEFDIS EDEPLWKKYI SQFKNPLIML LLASAVISVL MHQFDDAVSI TVAILIVVTV AFVQEYRSEK SLEELSKLVP PECHCVREGK LEHTLARDLV PGDTVCLSVG DRVPADLRLF EAVDLSIDES SLTGETTPCS KVTAPQPAAT NGDLASRSNI AFMGTLVRCG KAKGVVIGTG ENSEFGEVFK MMQAEEAPKT PLQKSMDLLG KQLSFYSFGI IGIIMLVGWL LGKDILEMFT ISVSLAVAAI PEGLPIVVTV TLALGVMRMV KKRAIVKKLP IVETLGCCNV ICSDKTGTLT KNEMTVTHIF TSDGLHAEVT GVGYNQFGEV IVDGDVVHGF YNPAVSRIVE AGCVCNDAVI RNNTLMGKPT EGALIALAMK MGLDGLQQDY IRKAEYPFSS EQKWMAVKCV HRTQQDRPEI CFMKGAYEQV IKYCTTYQSK GQTLTLTQQQ RDVYQQEKAR MGSAGLRVLA LASGPELGQL TFLGLVGIID PPRTGVKEAV TTLIASGVSI KMITGDSQET AVAIASRLGL YSKTSQSVSG EEIDAMDVQQ LSQIVPKVAV FYRASPRHKM KIIKSLQKNG SVVAMTGDGV NDAVALKAAD IGVAMGQTGT DVCKEAADMI LVDDDFQTIM SAIEEGKGIY NNIKNFVRFQ LSTSIAALTL ISLATLMNFP NPLNAMQILW INIIMDGPPA QSLGVEPVDK DVIRKPPRNW KDSILTKNLI LKILVSSIII VCGTLFVFWR ELRDNVITPR DTTMTFTCFV FFDMFNALSS RSQTKSVFEI GLCSNRMFCY AVLGSIMGQL LVIYFPPLQK VFQTESLSIL DLLFLLGLTS SVCIVAEIIK KVERSREKIQ KHVWLWERSG QQLVEIHPHL ETGLPLTEDV SCV* | ||||||||||||||||
| Mutated AA sequence | MIPVLTSKKA SELPVSEVAS ILQADLQNGL NKCEVSHRRA FHGWNEFDIS EDEPLWKKYI SQFKNPLIML LLASAVISVL MHQFDDAVSI TVAILIVVTV AFVQEYRSEK SLEELSKLVP PECHCVREGK LEHTLARDLV PGDTVCLSVG DRVPADLRLF EAVDLSIDES SLTGETTPCS KVTAPQPAAT NGDLASRSNI AFMGTLVRCG KAKGVVIGTG ENSEFGEVFK MMQAEEAPKT PLQKSMDLLG KQLSFYSFGI IGIIMLVGWL LGKDILEMFT ISVSLAVAAI PEGLPIVVTV TLALGVMRMV KKRAIVKKLP IVETLGCCNV ICSDKTGTLT KNEMTVTHIF TSDGLHAEVT GVGYNQFGEV IVDGDVVHGF YNPAVSRIVE AGCVCNDAVI RNNTLMGKPT EGALIALAMK MGLDGLQQDY IRKAEYPFSS EQKWMAVKCV HRTQQDRPEI CFMKGAYEQV IKYCTTYQSK GQTLTLTQQQ RDVYQQEKAR MGSAGLRVLA LASGPELGQL TFLGLVGIID PPRTGVKEAV TTLIASGVSI KMITGDSQET AVAIASRLGL YSKTSQSVSG EEIDAMDVQQ LSQIVPKVAV FYRASPRHKM KIIKSLQKNG SVVAMTGDGV NDAVALKAAD IGVAMGQTGT DVCKEAADMI LVDDDFQTIM SAIEEGKGIY SNIKNFVRFQ LSTSIAALTL ISLATLMNFP NPLNAMQILW INIIMDGPPA QSLGVEPVDK DVIRKPPRNW KDSILTKNLI LKILVSSIII VCGTLFVFWR ELRDNVITPR DTTMTFTCFV FFDMFNALSS RSQTKSVFEI GLCSNRMFCY AVLGSIMGQL LVIYFPPLQK VFQTESLSIL DLLFLLGLTS SVCIVAEIIK KVERSREKIQ KHVWLWERSG QQLVEIHPHL ETGLPLTEDV SCV* | ||||||||||||||||
| Position of stopcodon in wt / mu CDS | 2772 / 2772 | ||||||||||||||||
| Position (AA) of stopcodon in wt / mu AA sequence | 924 / 924 | ||||||||||||||||
| Position of stopcodon in wt / mu cDNA | 2974 / 2974 | ||||||||||||||||
| Position of start ATG in wt / mu cDNA | 203 / 203 | ||||||||||||||||
| Last intron/exon boundary | 2878 | ||||||||||||||||
| Theoretical NMD boundary in CDS | 2625 | ||||||||||||||||
| Length of CDS | 2772 | ||||||||||||||||
| Coding sequence (CDS) position | 2042 | ||||||||||||||||
| cDNA position | 2244 | ||||||||||||||||
| gDNA position | 145481 | ||||||||||||||||
| Chromosomal position | 130996075 | ||||||||||||||||
| Speed | 0.06 s | ||||||||||||||||
All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
| Analysed issue | Analysis result | ||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Variant | Chr3:130996075A>G (GRCh38) | ||||||||||||||||
| Gene symbol | ATP2C1 | ||||||||||||||||
| Gene constraints | LOEUF: 0.43, LOF (oe): 0.31, misssense (oe): 0.66, synonymous (oe): 0.89 (gnomAD) | ||||||||||||||||
| Ensembl transcript ID | ENST00000507488.6 | ||||||||||||||||
| Genbank transcript ID | NM_001378511 (by similarity), NM_001199180 (by similarity) | ||||||||||||||||
| UniProt / AlphaMissense peptide | AT2C1_HUMAN | AlphaMissense: transcript, gene | ||||||||||||||||
| Variant type | Single base exchange | ||||||||||||||||
| Gene region | CDS | ||||||||||||||||
| DNA changes | c.2192A>G g.145481A>G | ||||||||||||||||
| AA changes |
| ||||||||||||||||
| Frameshift | No | ||||||||||||||||
| Length of protein | Normal | ||||||||||||||||
| Pathogenic variant (ClinVar) | Variant not listed in ClinVar as (likely) pathogenic. | ||||||||||||||||
| Variant DBs |
| ||||||||||||||||
| Protein conservation | |||||||||||||||||
| Protein features |
| ||||||||||||||||
| Phylogenetic conservation |
| ||||||||||||||||
| Splice sites | No abrogation of potential splice sites predicted by MaxEntScan. | ||||||||||||||||
| Distance from splice site | N/A | ||||||||||||||||
| Kozak consensus sequence altered? | No | ||||||||||||||||
| poly(A) signal | N/A | ||||||||||||||||
| AA sequence altered | Yes | ||||||||||||||||
| Chromosome | 3 | ||||||||||||||||
| Strand | 1 | ||||||||||||||||
| Original gDNA sequence snippet | AGAGGGTAAAGGGATTTATAATAACATTAAAAATTTCGTTA | ||||||||||||||||
| Altered gDNA sequence snippet | AGAGGGTAAAGGGATTTATAGTAACATTAAAAATTTCGTTA | ||||||||||||||||
| Original cDNA sequence snippet | AGAGGGTAAAGGGATTTATAATAACATTAAAAATTTCGTTA | ||||||||||||||||
| Altered cDNA sequence snippet | AGAGGGTAAAGGGATTTATAGTAACATTAAAAATTTCGTTA | ||||||||||||||||
| Wildtype AA sequence | MDSLLPPSRF SYFKKYPLHA IRRYLSTLRN QRAEEQVARF QKIPNGENET MIPVLTSKKA SELPVSEVAS ILQADLQNGL NKCEVSHRRA FHGWNEFDIS EDEPLWKKYI SQFKNPLIML LLASAVISVL MHQFDDAVSI TVAILIVVTV AFVQEYRSEK SLEELSKLVP PECHCVREGK LEHTLARDLV PGDTVCLSVG DRVPADLRLF EAVDLSIDES SLTGETTPCS KVTAPQPAAT NGDLASRSNI AFMGTLVRCG KAKGVVIGTG ENSEFGEVFK MMQAEEAPKT PLQKSMDLLG KQLSFYSFGI IGIIMLVGWL LGKDILEMFT ISVSLAVAAI PEGLPIVVTV TLALGVMRMV KKRAIVKKLP IVETLGCCNV ICSDKTGTLT KNEMTVTHIF TSDGLHAEVT GVGYNQFGEV IVDGDVVHGF YNPAVSRIVE AGCVCNDAVI RNNTLMGKPT EGALIALAMK MGLDGLQQDY IRKAEYPFSS EQKWMAVKCV HRTQQDRPEI CFMKGAYEQV IKYCTTYQSK GQTLTLTQQQ RDVYQQEKAR MGSAGLRVLA LASGPELGQL TFLGLVGIID PPRTGVKEAV TTLIASGVSI KMITGDSQET AVAIASRLGL YSKTSQSVSG EEIDAMDVQQ LSQIVPKVAV FYRASPRHKM KIIKSLQKNG SVVAMTGDGV NDAVALKAAD IGVAMGQTGT DVCKEAADMI LVDDDFQTIM SAIEEGKGIY NNIKNFVRFQ LSTSIAALTL ISLATLMNFP NPLNAMQILW INIIMDGPPA QSLGVEPVDK DVIRKPPRNW KDSILTKNLI LKILVSSIII VCGTLFVFWR ELRDNVITPR DTTMTFTCFV FFDMFNALSS RSQTKSVFEI GLCSNRMFCY AVLGSIMGQL LVIYFPPLQK VFQTESLSIL DLLFLLGLTS SVCIVAEIIK KVERSREKIQ KHVWLWERSG QQLVEIHPHL ETGLPLTEDV SCV* | ||||||||||||||||
| Mutated AA sequence | MDSLLPPSRF SYFKKYPLHA IRRYLSTLRN QRAEEQVARF QKIPNGENET MIPVLTSKKA SELPVSEVAS ILQADLQNGL NKCEVSHRRA FHGWNEFDIS EDEPLWKKYI SQFKNPLIML LLASAVISVL MHQFDDAVSI TVAILIVVTV AFVQEYRSEK SLEELSKLVP PECHCVREGK LEHTLARDLV PGDTVCLSVG DRVPADLRLF EAVDLSIDES SLTGETTPCS KVTAPQPAAT NGDLASRSNI AFMGTLVRCG KAKGVVIGTG ENSEFGEVFK MMQAEEAPKT PLQKSMDLLG KQLSFYSFGI IGIIMLVGWL LGKDILEMFT ISVSLAVAAI PEGLPIVVTV TLALGVMRMV KKRAIVKKLP IVETLGCCNV ICSDKTGTLT KNEMTVTHIF TSDGLHAEVT GVGYNQFGEV IVDGDVVHGF YNPAVSRIVE AGCVCNDAVI RNNTLMGKPT EGALIALAMK MGLDGLQQDY IRKAEYPFSS EQKWMAVKCV HRTQQDRPEI CFMKGAYEQV IKYCTTYQSK GQTLTLTQQQ RDVYQQEKAR MGSAGLRVLA LASGPELGQL TFLGLVGIID PPRTGVKEAV TTLIASGVSI KMITGDSQET AVAIASRLGL YSKTSQSVSG EEIDAMDVQQ LSQIVPKVAV FYRASPRHKM KIIKSLQKNG SVVAMTGDGV NDAVALKAAD IGVAMGQTGT DVCKEAADMI LVDDDFQTIM SAIEEGKGIY SNIKNFVRFQ LSTSIAALTL ISLATLMNFP NPLNAMQILW INIIMDGPPA QSLGVEPVDK DVIRKPPRNW KDSILTKNLI LKILVSSIII VCGTLFVFWR ELRDNVITPR DTTMTFTCFV FFDMFNALSS RSQTKSVFEI GLCSNRMFCY AVLGSIMGQL LVIYFPPLQK VFQTESLSIL DLLFLLGLTS SVCIVAEIIK KVERSREKIQ KHVWLWERSG QQLVEIHPHL ETGLPLTEDV SCV* | ||||||||||||||||
| Position of stopcodon in wt / mu CDS | 2922 / 2922 | ||||||||||||||||
| Position (AA) of stopcodon in wt / mu AA sequence | 974 / 974 | ||||||||||||||||
| Position of stopcodon in wt / mu cDNA | 3142 / 3142 | ||||||||||||||||
| Position of start ATG in wt / mu cDNA | 221 / 221 | ||||||||||||||||
| Last intron/exon boundary | 3046 | ||||||||||||||||
| Theoretical NMD boundary in CDS | 2775 | ||||||||||||||||
| Length of CDS | 2922 | ||||||||||||||||
| Coding sequence (CDS) position | 2192 | ||||||||||||||||
| cDNA position | 2412 | ||||||||||||||||
| gDNA position | 145481 | ||||||||||||||||
| Chromosomal position | 130996075 | ||||||||||||||||
| Speed | 0.04 s | ||||||||||||||||
All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
| Analysed issue | Analysis result | ||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Variant | Chr3:130996075A>G (GRCh38) | ||||||||||||||||
| Gene symbol | ATP2C1 | ||||||||||||||||
| Gene constraints | LOEUF: 0.40, LOF (oe): 0.28, misssense (oe): 0.65, synonymous (oe): 0.89 (gnomAD) | ||||||||||||||||
| Ensembl transcript ID | ENST00000508532.5 | ||||||||||||||||
| Genbank transcript ID | NM_001199179 (by similarity) | ||||||||||||||||
| UniProt / AlphaMissense peptide | AT2C1_HUMAN | AlphaMissense: transcript, gene | ||||||||||||||||
| Variant type | Single base exchange | ||||||||||||||||
| Gene region | CDS | ||||||||||||||||
| DNA changes | c.2090A>G g.145481A>G | ||||||||||||||||
| AA changes |
| ||||||||||||||||
| Frameshift | No | ||||||||||||||||
| Length of protein | Normal | ||||||||||||||||
| Pathogenic variant (ClinVar) | Variant not listed in ClinVar as (likely) pathogenic. | ||||||||||||||||
| Variant DBs |
| ||||||||||||||||
| Protein conservation | |||||||||||||||||
| Protein features |
| ||||||||||||||||
| Phylogenetic conservation |
| ||||||||||||||||
| Splice sites | No abrogation of potential splice sites predicted by MaxEntScan. | ||||||||||||||||
| Distance from splice site | N/A | ||||||||||||||||
| Kozak consensus sequence altered? | No | ||||||||||||||||
| poly(A) signal | N/A | ||||||||||||||||
| AA sequence altered | Yes | ||||||||||||||||
| Chromosome | 3 | ||||||||||||||||
| Strand | 1 | ||||||||||||||||
| Original gDNA sequence snippet | AGAGGGTAAAGGGATTTATAATAACATTAAAAATTTCGTTA | ||||||||||||||||
| Altered gDNA sequence snippet | AGAGGGTAAAGGGATTTATAGTAACATTAAAAATTTCGTTA | ||||||||||||||||
| Original cDNA sequence snippet | AGAGGGTAAAGGGATTTATAATAACATTAAAAATTTCGTTA | ||||||||||||||||
| Altered cDNA sequence snippet | AGAGGGTAAAGGGATTTATAGTAACATTAAAAATTTCGTTA | ||||||||||||||||
| Wildtype AA sequence | MKVARFQKIP NGENETMIPV LTSKKASELP VSEVASILQA DLQNGLNKCE VSHRRAFHGW NEFDISEDEP LWKKYISQFK NPLIMLLLAS AVISVLMHQF DDAVSITVAI LIVVTVAFVQ EYRSEKSLEE LSKLVPPECH CVREGKLEHT LARDLVPGDT VCLSVGDRVP ADLRLFEAVD LSIDESSLTG ETTPCSKVTA PQPAATNGDL ASRSNIAFMG TLVRCGKAKG VVIGTGENSE FGEVFKMMQA EEAPKTPLQK SMDLLGKQLS FYSFGIIGII MLVGWLLGKD ILEMFTISVS LAVAAIPEGL PIVVTVTLAL GVMRMVKKRA IVKKLPIVET LGCCNVICSD KTGTLTKNEM TVTHIFTSDG LHAEVTGVGY NQFGEVIVDG DVVHGFYNPA VSRIVEAGCV CNDAVIRNNT LMGKPTEGAL IALAMKMGLD GLQQDYIRKA EYPFSSEQKW MAVKCVHRTQ QDRPEICFMK GAYEQVIKYC TTYQSKGQTL TLTQQQRDVY QQEKARMGSA GLRVLALASG PELGQLTFLG LVGIIDPPRT GVKEAVTTLI ASGVSIKMIT GDSQETAVAI ASRLGLYSKT SQSVSGEEID AMDVQQLSQI VPKVAVFYRA SPRHKMKIIK SLQKNGSVVA MTGDGVNDAV ALKAADIGVA MGQTGTDVCK EAADMILVDD DFQTIMSAIE EGKGIYNNIK NFVRFQLSTS IAALTLISLA TLMNFPNPLN AMQILWINII MDGPPAQSLG VEPVDKDVIR KPPRNWKDSI LTKNLILKIL VSSIIIVCGT LFVFWRELRD NVITPRDTTM TFTCFVFFDM FNALSSRSQT KSVFEIGLCS NRMFCYAVLG SIMGQLLVIY FPPLQKVFQT ESLSILDLLF LLGLTSSVCI VAEIIKKVER SREKIQKHVS STSSSFLEV* | ||||||||||||||||
| Mutated AA sequence | MKVARFQKIP NGENETMIPV LTSKKASELP VSEVASILQA DLQNGLNKCE VSHRRAFHGW NEFDISEDEP LWKKYISQFK NPLIMLLLAS AVISVLMHQF DDAVSITVAI LIVVTVAFVQ EYRSEKSLEE LSKLVPPECH CVREGKLEHT LARDLVPGDT VCLSVGDRVP ADLRLFEAVD LSIDESSLTG ETTPCSKVTA PQPAATNGDL ASRSNIAFMG TLVRCGKAKG VVIGTGENSE FGEVFKMMQA EEAPKTPLQK SMDLLGKQLS FYSFGIIGII MLVGWLLGKD ILEMFTISVS LAVAAIPEGL PIVVTVTLAL GVMRMVKKRA IVKKLPIVET LGCCNVICSD KTGTLTKNEM TVTHIFTSDG LHAEVTGVGY NQFGEVIVDG DVVHGFYNPA VSRIVEAGCV CNDAVIRNNT LMGKPTEGAL IALAMKMGLD GLQQDYIRKA EYPFSSEQKW MAVKCVHRTQ QDRPEICFMK GAYEQVIKYC TTYQSKGQTL TLTQQQRDVY QQEKARMGSA GLRVLALASG PELGQLTFLG LVGIIDPPRT GVKEAVTTLI ASGVSIKMIT GDSQETAVAI ASRLGLYSKT SQSVSGEEID AMDVQQLSQI VPKVAVFYRA SPRHKMKIIK SLQKNGSVVA MTGDGVNDAV ALKAADIGVA MGQTGTDVCK EAADMILVDD DFQTIMSAIE EGKGIYSNIK NFVRFQLSTS IAALTLISLA TLMNFPNPLN AMQILWINII MDGPPAQSLG VEPVDKDVIR KPPRNWKDSI LTKNLILKIL VSSIIIVCGT LFVFWRELRD NVITPRDTTM TFTCFVFFDM FNALSSRSQT KSVFEIGLCS NRMFCYAVLG SIMGQLLVIY FPPLQKVFQT ESLSILDLLF LLGLTSSVCI VAEIIKKVER SREKIQKHVS STSSSFLEV* | ||||||||||||||||
| Position of stopcodon in wt / mu CDS | 2760 / 2760 | ||||||||||||||||
| Position (AA) of stopcodon in wt / mu AA sequence | 920 / 920 | ||||||||||||||||
| Position of stopcodon in wt / mu cDNA | 3169 / 3169 | ||||||||||||||||
| Position of start ATG in wt / mu cDNA | 410 / 410 | ||||||||||||||||
| Last intron/exon boundary | 3038 | ||||||||||||||||
| Theoretical NMD boundary in CDS | 2578 | ||||||||||||||||
| Length of CDS | 2760 | ||||||||||||||||
| Coding sequence (CDS) position | 2090 | ||||||||||||||||
| cDNA position | 2499 | ||||||||||||||||
| gDNA position | 145481 | ||||||||||||||||
| Chromosomal position | 130996075 | ||||||||||||||||
| Speed | 0.06 s | ||||||||||||||||
All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
| Analysed issue | Analysis result | ||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Variant | Chr3:130996075A>G (GRCh38) | ||||||||||||||||
| Gene symbol | ATP2C1 | ||||||||||||||||
| Gene constraints | LOEUF: 0.40, LOF (oe): 0.28, misssense (oe): 0.65, synonymous (oe): 0.89 (gnomAD) | ||||||||||||||||
| Ensembl transcript ID | ENST00000428331.6 | ||||||||||||||||
| Genbank transcript ID | NM_014382 (by similarity) | ||||||||||||||||
| UniProt / AlphaMissense peptide | AT2C1_HUMAN | AlphaMissense: transcript, gene | ||||||||||||||||
| Variant type | Single base exchange | ||||||||||||||||
| Gene region | CDS | ||||||||||||||||
| DNA changes | c.2090A>G g.145481A>G | ||||||||||||||||
| AA changes |
| ||||||||||||||||
| Frameshift | No | ||||||||||||||||
| Length of protein | Normal | ||||||||||||||||
| Pathogenic variant (ClinVar) | Variant not listed in ClinVar as (likely) pathogenic. | ||||||||||||||||
| Variant DBs |
| ||||||||||||||||
| Protein conservation | |||||||||||||||||
| Protein features |
| ||||||||||||||||
| Phylogenetic conservation |
| ||||||||||||||||
| Splice sites | No abrogation of potential splice sites predicted by MaxEntScan. | ||||||||||||||||
| Distance from splice site | N/A | ||||||||||||||||
| Kozak consensus sequence altered? | No | ||||||||||||||||
| poly(A) signal | N/A | ||||||||||||||||
| AA sequence altered | Yes | ||||||||||||||||
| Chromosome | 3 | ||||||||||||||||
| Strand | 1 | ||||||||||||||||
| Original gDNA sequence snippet | AGAGGGTAAAGGGATTTATAATAACATTAAAAATTTCGTTA | ||||||||||||||||
| Altered gDNA sequence snippet | AGAGGGTAAAGGGATTTATAGTAACATTAAAAATTTCGTTA | ||||||||||||||||
| Original cDNA sequence snippet | AGAGGGTAAAGGGATTTATAATAACATTAAAAATTTCGTTA | ||||||||||||||||
| Altered cDNA sequence snippet | AGAGGGTAAAGGGATTTATAGTAACATTAAAAATTTCGTTA | ||||||||||||||||
| Wildtype AA sequence | MKVARFQKIP NGENETMIPV LTSKKASELP VSEVASILQA DLQNGLNKCE VSHRRAFHGW NEFDISEDEP LWKKYISQFK NPLIMLLLAS AVISVLMHQF DDAVSITVAI LIVVTVAFVQ EYRSEKSLEE LSKLVPPECH CVREGKLEHT LARDLVPGDT VCLSVGDRVP ADLRLFEAVD LSIDESSLTG ETTPCSKVTA PQPAATNGDL ASRSNIAFMG TLVRCGKAKG VVIGTGENSE FGEVFKMMQA EEAPKTPLQK SMDLLGKQLS FYSFGIIGII MLVGWLLGKD ILEMFTISVS LAVAAIPEGL PIVVTVTLAL GVMRMVKKRA IVKKLPIVET LGCCNVICSD KTGTLTKNEM TVTHIFTSDG LHAEVTGVGY NQFGEVIVDG DVVHGFYNPA VSRIVEAGCV CNDAVIRNNT LMGKPTEGAL IALAMKMGLD GLQQDYIRKA EYPFSSEQKW MAVKCVHRTQ QDRPEICFMK GAYEQVIKYC TTYQSKGQTL TLTQQQRDVY QQEKARMGSA GLRVLALASG PELGQLTFLG LVGIIDPPRT GVKEAVTTLI ASGVSIKMIT GDSQETAVAI ASRLGLYSKT SQSVSGEEID AMDVQQLSQI VPKVAVFYRA SPRHKMKIIK SLQKNGSVVA MTGDGVNDAV ALKAADIGVA MGQTGTDVCK EAADMILVDD DFQTIMSAIE EGKGIYNNIK NFVRFQLSTS IAALTLISLA TLMNFPNPLN AMQILWINII MDGPPAQSLG VEPVDKDVIR KPPRNWKDSI LTKNLILKIL VSSIIIVCGT LFVFWRELRD NVITPRDTTM TFTCFVFFDM FNALSSRSQT KSVFEIGLCS NRMFCYAVLG SIMGQLLVIY FPPLQKVFQT ESLSILDLLF LLGLTSSVCI VAEIIKKVER SREKIQKHVS STSSSFLEV* | ||||||||||||||||
| Mutated AA sequence | MKVARFQKIP NGENETMIPV LTSKKASELP VSEVASILQA DLQNGLNKCE VSHRRAFHGW NEFDISEDEP LWKKYISQFK NPLIMLLLAS AVISVLMHQF DDAVSITVAI LIVVTVAFVQ EYRSEKSLEE LSKLVPPECH CVREGKLEHT LARDLVPGDT VCLSVGDRVP ADLRLFEAVD LSIDESSLTG ETTPCSKVTA PQPAATNGDL ASRSNIAFMG TLVRCGKAKG VVIGTGENSE FGEVFKMMQA EEAPKTPLQK SMDLLGKQLS FYSFGIIGII MLVGWLLGKD ILEMFTISVS LAVAAIPEGL PIVVTVTLAL GVMRMVKKRA IVKKLPIVET LGCCNVICSD KTGTLTKNEM TVTHIFTSDG LHAEVTGVGY NQFGEVIVDG DVVHGFYNPA VSRIVEAGCV CNDAVIRNNT LMGKPTEGAL IALAMKMGLD GLQQDYIRKA EYPFSSEQKW MAVKCVHRTQ QDRPEICFMK GAYEQVIKYC TTYQSKGQTL TLTQQQRDVY QQEKARMGSA GLRVLALASG PELGQLTFLG LVGIIDPPRT GVKEAVTTLI ASGVSIKMIT GDSQETAVAI ASRLGLYSKT SQSVSGEEID AMDVQQLSQI VPKVAVFYRA SPRHKMKIIK SLQKNGSVVA MTGDGVNDAV ALKAADIGVA MGQTGTDVCK EAADMILVDD DFQTIMSAIE EGKGIYSNIK NFVRFQLSTS IAALTLISLA TLMNFPNPLN AMQILWINII MDGPPAQSLG VEPVDKDVIR KPPRNWKDSI LTKNLILKIL VSSIIIVCGT LFVFWRELRD NVITPRDTTM TFTCFVFFDM FNALSSRSQT KSVFEIGLCS NRMFCYAVLG SIMGQLLVIY FPPLQKVFQT ESLSILDLLF LLGLTSSVCI VAEIIKKVER SREKIQKHVS STSSSFLEV* | ||||||||||||||||
| Position of stopcodon in wt / mu CDS | 2760 / 2760 | ||||||||||||||||
| Position (AA) of stopcodon in wt / mu AA sequence | 920 / 920 | ||||||||||||||||
| Position of stopcodon in wt / mu cDNA | 2995 / 2995 | ||||||||||||||||
| Position of start ATG in wt / mu cDNA | 236 / 236 | ||||||||||||||||
| Last intron/exon boundary | 2864 | ||||||||||||||||
| Theoretical NMD boundary in CDS | 2578 | ||||||||||||||||
| Length of CDS | 2760 | ||||||||||||||||
| Coding sequence (CDS) position | 2090 | ||||||||||||||||
| cDNA position | 2325 | ||||||||||||||||
| gDNA position | 145481 | ||||||||||||||||
| Chromosomal position | 130996075 | ||||||||||||||||
| Speed | 0.06 s | ||||||||||||||||
All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
| Analysed issue | Analysis result | ||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Variant | Chr3:130996075A>G (GRCh38) | ||||||||||||||||
| Gene symbol | ATP2C1 | ||||||||||||||||
| Gene constraints | LOEUF: 0.44, LOF (oe): 0.32, misssense (oe): 0.65, synonymous (oe): 0.89 (gnomAD) | ||||||||||||||||
| Ensembl transcript ID | ENST00000359644.7 | ||||||||||||||||
| Genbank transcript ID | NM_001001486 (by similarity), NM_001378512 (by similarity) | ||||||||||||||||
| UniProt / AlphaMissense peptide | AT2C1_HUMAN | AlphaMissense: transcript, gene | ||||||||||||||||
| Variant type | Single base exchange | ||||||||||||||||
| Gene region | CDS | ||||||||||||||||
| DNA changes | c.2090A>G g.145481A>G | ||||||||||||||||
| AA changes |
| ||||||||||||||||
| Frameshift | No | ||||||||||||||||
| Length of protein | Normal | ||||||||||||||||
| Pathogenic variant (ClinVar) | Variant not listed in ClinVar as (likely) pathogenic. | ||||||||||||||||
| Variant DBs |
| ||||||||||||||||
| Protein conservation | |||||||||||||||||
| Protein features |
| ||||||||||||||||
| Phylogenetic conservation |
| ||||||||||||||||
| Splice sites | No abrogation of potential splice sites predicted by MaxEntScan. | ||||||||||||||||
| Distance from splice site | N/A | ||||||||||||||||
| Kozak consensus sequence altered? | No | ||||||||||||||||
| poly(A) signal | N/A | ||||||||||||||||
| AA sequence altered | Yes | ||||||||||||||||
| Chromosome | 3 | ||||||||||||||||
| Strand | 1 | ||||||||||||||||
| Original gDNA sequence snippet | AGAGGGTAAAGGGATTTATAATAACATTAAAAATTTCGTTA | ||||||||||||||||
| Altered gDNA sequence snippet | AGAGGGTAAAGGGATTTATAGTAACATTAAAAATTTCGTTA | ||||||||||||||||
| Original cDNA sequence snippet | AGAGGGTAAAGGGATTTATAATAACATTAAAAATTTCGTTA | ||||||||||||||||
| Altered cDNA sequence snippet | AGAGGGTAAAGGGATTTATAGTAACATTAAAAATTTCGTTA | ||||||||||||||||
| Wildtype AA sequence | MKVARFQKIP NGENETMIPV LTSKKASELP VSEVASILQA DLQNGLNKCE VSHRRAFHGW NEFDISEDEP LWKKYISQFK NPLIMLLLAS AVISVLMHQF DDAVSITVAI LIVVTVAFVQ EYRSEKSLEE LSKLVPPECH CVREGKLEHT LARDLVPGDT VCLSVGDRVP ADLRLFEAVD LSIDESSLTG ETTPCSKVTA PQPAATNGDL ASRSNIAFMG TLVRCGKAKG VVIGTGENSE FGEVFKMMQA EEAPKTPLQK SMDLLGKQLS FYSFGIIGII MLVGWLLGKD ILEMFTISVS LAVAAIPEGL PIVVTVTLAL GVMRMVKKRA IVKKLPIVET LGCCNVICSD KTGTLTKNEM TVTHIFTSDG LHAEVTGVGY NQFGEVIVDG DVVHGFYNPA VSRIVEAGCV CNDAVIRNNT LMGKPTEGAL IALAMKMGLD GLQQDYIRKA EYPFSSEQKW MAVKCVHRTQ QDRPEICFMK GAYEQVIKYC TTYQSKGQTL TLTQQQRDVY QQEKARMGSA GLRVLALASG PELGQLTFLG LVGIIDPPRT GVKEAVTTLI ASGVSIKMIT GDSQETAVAI ASRLGLYSKT SQSVSGEEID AMDVQQLSQI VPKVAVFYRA SPRHKMKIIK SLQKNGSVVA MTGDGVNDAV ALKAADIGVA MGQTGTDVCK EAADMILVDD DFQTIMSAIE EGKGIYNNIK NFVRFQLSTS IAALTLISLA TLMNFPNPLN AMQILWINII MDGPPAQSLG VEPVDKDVIR KPPRNWKDSI LTKNLILKIL VSSIIIVCGT LFVFWRELRD NVITPRDTTM TFTCFVFFDM FNALSSRSQT KSVFEIGLCS NRMFCYAVLG SIMGQLLVIY FPPLQKVFQT ESLSILDLLF LLGLTSSVCI VAEIIKKVER SREKIQKHVS STSSSFLEVW LWERSGQQLV EIHPHLETGL PLTEDVSCV* | ||||||||||||||||
| Mutated AA sequence | MKVARFQKIP NGENETMIPV LTSKKASELP VSEVASILQA DLQNGLNKCE VSHRRAFHGW NEFDISEDEP LWKKYISQFK NPLIMLLLAS AVISVLMHQF DDAVSITVAI LIVVTVAFVQ EYRSEKSLEE LSKLVPPECH CVREGKLEHT LARDLVPGDT VCLSVGDRVP ADLRLFEAVD LSIDESSLTG ETTPCSKVTA PQPAATNGDL ASRSNIAFMG TLVRCGKAKG VVIGTGENSE FGEVFKMMQA EEAPKTPLQK SMDLLGKQLS FYSFGIIGII MLVGWLLGKD ILEMFTISVS LAVAAIPEGL PIVVTVTLAL GVMRMVKKRA IVKKLPIVET LGCCNVICSD KTGTLTKNEM TVTHIFTSDG LHAEVTGVGY NQFGEVIVDG DVVHGFYNPA VSRIVEAGCV CNDAVIRNNT LMGKPTEGAL IALAMKMGLD GLQQDYIRKA EYPFSSEQKW MAVKCVHRTQ QDRPEICFMK GAYEQVIKYC TTYQSKGQTL TLTQQQRDVY QQEKARMGSA GLRVLALASG PELGQLTFLG LVGIIDPPRT GVKEAVTTLI ASGVSIKMIT GDSQETAVAI ASRLGLYSKT SQSVSGEEID AMDVQQLSQI VPKVAVFYRA SPRHKMKIIK SLQKNGSVVA MTGDGVNDAV ALKAADIGVA MGQTGTDVCK EAADMILVDD DFQTIMSAIE EGKGIYSNIK NFVRFQLSTS IAALTLISLA TLMNFPNPLN AMQILWINII MDGPPAQSLG VEPVDKDVIR KPPRNWKDSI LTKNLILKIL VSSIIIVCGT LFVFWRELRD NVITPRDTTM TFTCFVFFDM FNALSSRSQT KSVFEIGLCS NRMFCYAVLG SIMGQLLVIY FPPLQKVFQT ESLSILDLLF LLGLTSSVCI VAEIIKKVER SREKIQKHVS STSSSFLEVW LWERSGQQLV EIHPHLETGL PLTEDVSCV* | ||||||||||||||||
| Position of stopcodon in wt / mu CDS | 2850 / 2850 | ||||||||||||||||
| Position (AA) of stopcodon in wt / mu AA sequence | 950 / 950 | ||||||||||||||||
| Position of stopcodon in wt / mu cDNA | 2979 / 2979 | ||||||||||||||||
| Position of start ATG in wt / mu cDNA | 130 / 130 | ||||||||||||||||
| Last intron/exon boundary | 2883 | ||||||||||||||||
| Theoretical NMD boundary in CDS | 2703 | ||||||||||||||||
| Length of CDS | 2850 | ||||||||||||||||
| Coding sequence (CDS) position | 2090 | ||||||||||||||||
| cDNA position | 2219 | ||||||||||||||||
| gDNA position | 145481 | ||||||||||||||||
| Chromosomal position | 130996075 | ||||||||||||||||
| Speed | 0.05 s | ||||||||||||||||
All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
| Analysed issue | Analysis result | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Variant | Chr3:130996075A>G (GRCh38) | |||||||||||||
| Gene symbol | ATP2C1 | |||||||||||||
| Gene constraints | LOEUF: 0.39, LOF (oe): 0.27, misssense (oe): 0.65, synonymous (oe): 0.89 (gnomAD) | |||||||||||||
| Ensembl transcript ID | ENST00000505330.5 | |||||||||||||
| Genbank transcript ID | NM_001199181 (by similarity) | |||||||||||||
| UniProt / AlphaMissense peptide | N/A | |||||||||||||
| Variant type | Single base exchange | |||||||||||||
| Gene region | CDS | |||||||||||||
| DNA changes | c.2192A>G g.145481A>G | |||||||||||||
| AA changes |
| |||||||||||||
| Frameshift | No | |||||||||||||
| Length of protein | Normal | |||||||||||||
| Pathogenic variant (ClinVar) | Variant not listed in ClinVar as (likely) pathogenic. | |||||||||||||
| Variant DBs |
| |||||||||||||
| Protein conservation | ||||||||||||||
| Protein features | N/A | |||||||||||||
| Phylogenetic conservation |
| |||||||||||||
| Splice sites | No abrogation of potential splice sites predicted by MaxEntScan. | |||||||||||||
| Distance from splice site | N/A | |||||||||||||
| Kozak consensus sequence altered? | No | |||||||||||||
| poly(A) signal | N/A | |||||||||||||
| AA sequence altered | Yes | |||||||||||||
| Chromosome | 3 | |||||||||||||
| Strand | 1 | |||||||||||||
| Original gDNA sequence snippet | AGAGGGTAAAGGGATTTATAATAACATTAAAAATTTCGTTA | |||||||||||||
| Altered gDNA sequence snippet | AGAGGGTAAAGGGATTTATAGTAACATTAAAAATTTCGTTA | |||||||||||||
| Original cDNA sequence snippet | AGAGGGTAAAGGGATTTATAATAACATTAAAAATTTCGTTA | |||||||||||||
| Altered cDNA sequence snippet | AGAGGGTAAAGGGATTTATAGTAACATTAAAAATTTCGTTA | |||||||||||||
| Wildtype AA sequence | MDSLLPPSRF SYFKKYPLHA IRRYLSTLRN QRAEEQVARF QKIPNGENET MIPVLTSKKA SELPVSEVAS ILQADLQNGL NKCEVSHRRA FHGWNEFDIS EDEPLWKKYI SQFKNPLIML LLASAVISVL MHQFDDAVSI TVAILIVVTV AFVQEYRSEK SLEELSKLVP PECHCVREGK LEHTLARDLV PGDTVCLSVG DRVPADLRLF EAVDLSIDES SLTGETTPCS KVTAPQPAAT NGDLASRSNI AFMGTLVRCG KAKGVVIGTG ENSEFGEVFK MMQAEEAPKT PLQKSMDLLG KQLSFYSFGI IGIIMLVGWL LGKDILEMFT ISVSLAVAAI PEGLPIVVTV TLALGVMRMV KKRAIVKKLP IVETLGCCNV ICSDKTGTLT KNEMTVTHIF TSDGLHAEVT GVGYNQFGEV IVDGDVVHGF YNPAVSRIVE AGCVCNDAVI RNNTLMGKPT EGALIALAMK MGLDGLQQDY IRKAEYPFSS EQKWMAVKCV HRTQQDRPEI CFMKGAYEQV IKYCTTYQSK GQTLTLTQQQ RDVYQQEKAR MGSAGLRVLA LASGPELGQL TFLGLVGIID PPRTGVKEAV TTLIASGVSI KMITGDSQET AVAIASRLGL YSKTSQSVSG EEIDAMDVQQ LSQIVPKVAV FYRASPRHKM KIIKSLQKNG SVVAMTGDGV NDAVALKAAD IGVAMGQTGT DVCKEAADMI LVDDDFQTIM SAIEEGKGIY NNIKNFVRFQ LSTSIAALTL ISLATLMNFP NPLNAMQILW INIIMDGPPA QSLGVEPVDK DVIRKPPRNW KDSILTKNLI LKILVSSIII VCGTLFVFWR ELRDNVITPR DTTMTFTCFV FFDMFNALSS RSQTKSVFEI GLCSNRMFCY AVLGSIMGQL LVIYFPPLQK VFQTESLSIL DLLFLLGLTS SVCIVAEIIK KVERSREKIQ KHVSSTSSSF LEV* | |||||||||||||
| Mutated AA sequence | MDSLLPPSRF SYFKKYPLHA IRRYLSTLRN QRAEEQVARF QKIPNGENET MIPVLTSKKA SELPVSEVAS ILQADLQNGL NKCEVSHRRA FHGWNEFDIS EDEPLWKKYI SQFKNPLIML LLASAVISVL MHQFDDAVSI TVAILIVVTV AFVQEYRSEK SLEELSKLVP PECHCVREGK LEHTLARDLV PGDTVCLSVG DRVPADLRLF EAVDLSIDES SLTGETTPCS KVTAPQPAAT NGDLASRSNI AFMGTLVRCG KAKGVVIGTG ENSEFGEVFK MMQAEEAPKT PLQKSMDLLG KQLSFYSFGI IGIIMLVGWL LGKDILEMFT ISVSLAVAAI PEGLPIVVTV TLALGVMRMV KKRAIVKKLP IVETLGCCNV ICSDKTGTLT KNEMTVTHIF TSDGLHAEVT GVGYNQFGEV IVDGDVVHGF YNPAVSRIVE AGCVCNDAVI RNNTLMGKPT EGALIALAMK MGLDGLQQDY IRKAEYPFSS EQKWMAVKCV HRTQQDRPEI CFMKGAYEQV IKYCTTYQSK GQTLTLTQQQ RDVYQQEKAR MGSAGLRVLA LASGPELGQL TFLGLVGIID PPRTGVKEAV TTLIASGVSI KMITGDSQET AVAIASRLGL YSKTSQSVSG EEIDAMDVQQ LSQIVPKVAV FYRASPRHKM KIIKSLQKNG SVVAMTGDGV NDAVALKAAD IGVAMGQTGT DVCKEAADMI LVDDDFQTIM SAIEEGKGIY SNIKNFVRFQ LSTSIAALTL ISLATLMNFP NPLNAMQILW INIIMDGPPA QSLGVEPVDK DVIRKPPRNW KDSILTKNLI LKILVSSIII VCGTLFVFWR ELRDNVITPR DTTMTFTCFV FFDMFNALSS RSQTKSVFEI GLCSNRMFCY AVLGSIMGQL LVIYFPPLQK VFQTESLSIL DLLFLLGLTS SVCIVAEIIK KVERSREKIQ KHVSSTSSSF LEV* | |||||||||||||
| Position of stopcodon in wt / mu CDS | 2862 / 2862 | |||||||||||||
| Position (AA) of stopcodon in wt / mu AA sequence | 954 / 954 | |||||||||||||
| Position of stopcodon in wt / mu cDNA | 3088 / 3088 | |||||||||||||
| Position of start ATG in wt / mu cDNA | 227 / 227 | |||||||||||||
| Last intron/exon boundary | 2957 | |||||||||||||
| Theoretical NMD boundary in CDS | 2680 | |||||||||||||
| Length of CDS | 2862 | |||||||||||||
| Coding sequence (CDS) position | 2192 | |||||||||||||
| cDNA position | 2418 | |||||||||||||
| gDNA position | 145481 | |||||||||||||
| Chromosomal position | 130996075 | |||||||||||||
| Speed | 0.05 s | |||||||||||||
All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
| Analysed issue | Analysis result | ||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Variant | Chr3:130996075A>G (GRCh38) | ||||||||||||||||
| Gene symbol | ATP2C1 | ||||||||||||||||
| Gene constraints | LOEUF: 0.40, LOF (oe): 0.28, misssense (oe): 0.65, synonymous (oe): 0.89 (gnomAD) | ||||||||||||||||
| Ensembl transcript ID | ENST00000504948.5 | ||||||||||||||||
| Genbank transcript ID | NM_001199184 (by similarity) | ||||||||||||||||
| UniProt / AlphaMissense peptide | AT2C1_HUMAN | AlphaMissense: transcript, gene | ||||||||||||||||
| Variant type | Single base exchange | ||||||||||||||||
| Gene region | CDS | ||||||||||||||||
| DNA changes | c.2042A>G g.145481A>G | ||||||||||||||||
| AA changes |
| ||||||||||||||||
| Frameshift | No | ||||||||||||||||
| Length of protein | Normal | ||||||||||||||||
| Pathogenic variant (ClinVar) | Variant not listed in ClinVar as (likely) pathogenic. | ||||||||||||||||
| Variant DBs |
| ||||||||||||||||
| Protein conservation | |||||||||||||||||
| Protein features |
| ||||||||||||||||
| Phylogenetic conservation |
| ||||||||||||||||
| Splice sites | No abrogation of potential splice sites predicted by MaxEntScan. | ||||||||||||||||
| Distance from splice site | N/A | ||||||||||||||||
| Kozak consensus sequence altered? | No | ||||||||||||||||
| poly(A) signal | N/A | ||||||||||||||||
| AA sequence altered | Yes | ||||||||||||||||
| Chromosome | 3 | ||||||||||||||||
| Strand | 1 | ||||||||||||||||
| Original gDNA sequence snippet | AGAGGGTAAAGGGATTTATAATAACATTAAAAATTTCGTTA | ||||||||||||||||
| Altered gDNA sequence snippet | AGAGGGTAAAGGGATTTATAGTAACATTAAAAATTTCGTTA | ||||||||||||||||
| Original cDNA sequence snippet | AGAGGGTAAAGGGATTTATAATAACATTAAAAATTTCGTTA | ||||||||||||||||
| Altered cDNA sequence snippet | AGAGGGTAAAGGGATTTATAGTAACATTAAAAATTTCGTTA | ||||||||||||||||
| Wildtype AA sequence | MIPVLTSKKA SELPVSEVAS ILQADLQNGL NKCEVSHRRA FHGWNEFDIS EDEPLWKKYI SQFKNPLIML LLASAVISVL MHQFDDAVSI TVAILIVVTV AFVQEYRSEK SLEELSKLVP PECHCVREGK LEHTLARDLV PGDTVCLSVG DRVPADLRLF EAVDLSIDES SLTGETTPCS KVTAPQPAAT NGDLASRSNI AFMGTLVRCG KAKGVVIGTG ENSEFGEVFK MMQAEEAPKT PLQKSMDLLG KQLSFYSFGI IGIIMLVGWL LGKDILEMFT ISVSLAVAAI PEGLPIVVTV TLALGVMRMV KKRAIVKKLP IVETLGCCNV ICSDKTGTLT KNEMTVTHIF TSDGLHAEVT GVGYNQFGEV IVDGDVVHGF YNPAVSRIVE AGCVCNDAVI RNNTLMGKPT EGALIALAMK MGLDGLQQDY IRKAEYPFSS EQKWMAVKCV HRTQQDRPEI CFMKGAYEQV IKYCTTYQSK GQTLTLTQQQ RDVYQQEKAR MGSAGLRVLA LASGPELGQL TFLGLVGIID PPRTGVKEAV TTLIASGVSI KMITGDSQET AVAIASRLGL YSKTSQSVSG EEIDAMDVQQ LSQIVPKVAV FYRASPRHKM KIIKSLQKNG SVVAMTGDGV NDAVALKAAD IGVAMGQTGT DVCKEAADMI LVDDDFQTIM SAIEEGKGIY NNIKNFVRFQ LSTSIAALTL ISLATLMNFP NPLNAMQILW INIIMDGPPA QSLGVEPVDK DVIRKPPRNW KDSILTKNLI LKILVSSIII VCGTLFVFWR ELRDNVITPR DTTMTFTCFV FFDMFNALSS RSQTKSVFEI GLCSNRMFCY AVLGSIMGQL LVIYFPPLQK VFQTESLSIL DLLFLLGLTS SVCIVAEIIK KVERSREKIQ KHVSSTSSSF LEV* | ||||||||||||||||
| Mutated AA sequence | MIPVLTSKKA SELPVSEVAS ILQADLQNGL NKCEVSHRRA FHGWNEFDIS EDEPLWKKYI SQFKNPLIML LLASAVISVL MHQFDDAVSI TVAILIVVTV AFVQEYRSEK SLEELSKLVP PECHCVREGK LEHTLARDLV PGDTVCLSVG DRVPADLRLF EAVDLSIDES SLTGETTPCS KVTAPQPAAT NGDLASRSNI AFMGTLVRCG KAKGVVIGTG ENSEFGEVFK MMQAEEAPKT PLQKSMDLLG KQLSFYSFGI IGIIMLVGWL LGKDILEMFT ISVSLAVAAI PEGLPIVVTV TLALGVMRMV KKRAIVKKLP IVETLGCCNV ICSDKTGTLT KNEMTVTHIF TSDGLHAEVT GVGYNQFGEV IVDGDVVHGF YNPAVSRIVE AGCVCNDAVI RNNTLMGKPT EGALIALAMK MGLDGLQQDY IRKAEYPFSS EQKWMAVKCV HRTQQDRPEI CFMKGAYEQV IKYCTTYQSK GQTLTLTQQQ RDVYQQEKAR MGSAGLRVLA LASGPELGQL TFLGLVGIID PPRTGVKEAV TTLIASGVSI KMITGDSQET AVAIASRLGL YSKTSQSVSG EEIDAMDVQQ LSQIVPKVAV FYRASPRHKM KIIKSLQKNG SVVAMTGDGV NDAVALKAAD IGVAMGQTGT DVCKEAADMI LVDDDFQTIM SAIEEGKGIY SNIKNFVRFQ LSTSIAALTL ISLATLMNFP NPLNAMQILW INIIMDGPPA QSLGVEPVDK DVIRKPPRNW KDSILTKNLI LKILVSSIII VCGTLFVFWR ELRDNVITPR DTTMTFTCFV FFDMFNALSS RSQTKSVFEI GLCSNRMFCY AVLGSIMGQL LVIYFPPLQK VFQTESLSIL DLLFLLGLTS SVCIVAEIIK KVERSREKIQ KHVSSTSSSF LEV* | ||||||||||||||||
| Position of stopcodon in wt / mu CDS | 2712 / 2712 | ||||||||||||||||
| Position (AA) of stopcodon in wt / mu AA sequence | 904 / 904 | ||||||||||||||||
| Position of stopcodon in wt / mu cDNA | 2914 / 2914 | ||||||||||||||||
| Position of start ATG in wt / mu cDNA | 203 / 203 | ||||||||||||||||
| Last intron/exon boundary | 2783 | ||||||||||||||||
| Theoretical NMD boundary in CDS | 2530 | ||||||||||||||||
| Length of CDS | 2712 | ||||||||||||||||
| Coding sequence (CDS) position | 2042 | ||||||||||||||||
| cDNA position | 2244 | ||||||||||||||||
| gDNA position | 145481 | ||||||||||||||||
| Chromosomal position | 130996075 | ||||||||||||||||
| Speed | 0.03 s | ||||||||||||||||
All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
| Analysed issue | Analysis result | ||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Variant | Chr3:130996075A>G (GRCh38) | ||||||||||||||||
| Gene symbol | ATP2C1 | ||||||||||||||||
| Gene constraints | LOEUF: 0.42, LOF (oe): 0.30, misssense (oe): 0.65, synonymous (oe): 0.91 (gnomAD) | ||||||||||||||||
| Ensembl transcript ID | ENST00000504381.5 | ||||||||||||||||
| Genbank transcript ID | NM_001199182 (by similarity) | ||||||||||||||||
| UniProt / AlphaMissense peptide | AT2C1_HUMAN | AlphaMissense: transcript, gene | ||||||||||||||||
| Variant type | Single base exchange | ||||||||||||||||
| Gene region | CDS | ||||||||||||||||
| DNA changes | c.2075A>G g.145481A>G | ||||||||||||||||
| AA changes |
| ||||||||||||||||
| Frameshift | No | ||||||||||||||||
| Length of protein | Normal | ||||||||||||||||
| Pathogenic variant (ClinVar) | Variant not listed in ClinVar as (likely) pathogenic. | ||||||||||||||||
| Variant DBs |
| ||||||||||||||||
| Protein conservation | |||||||||||||||||
| Protein features |
| ||||||||||||||||
| Phylogenetic conservation |
| ||||||||||||||||
| Splice sites | No abrogation of potential splice sites predicted by MaxEntScan. | ||||||||||||||||
| Distance from splice site | N/A | ||||||||||||||||
| Kozak consensus sequence altered? | No | ||||||||||||||||
| poly(A) signal | N/A | ||||||||||||||||
| AA sequence altered | Yes | ||||||||||||||||
| Chromosome | 3 | ||||||||||||||||
| Strand | 1 | ||||||||||||||||
| Original gDNA sequence snippet | AGAGGGTAAAGGGATTTATAATAACATTAAAAATTTCGTTA | ||||||||||||||||
| Altered gDNA sequence snippet | AGAGGGTAAAGGGATTTATAGTAACATTAAAAATTTCGTTA | ||||||||||||||||
| Original cDNA sequence snippet | AGAGGGTAAAGGGATTTATAATAACATTAAAAATTTCGTTA | ||||||||||||||||
| Altered cDNA sequence snippet | AGAGGGTAAAGGGATTTATAGTAACATTAAAAATTTCGTTA | ||||||||||||||||
| Wildtype AA sequence | MDSLLPPSRF SYFKKYPLHA IRRYLSTLRN QRAEEQVARF QKIPNGENET MIPVLTSKKA SELPVSEVAS ILQFKNPLIM LLLASAVISV LMHQFDDAVS ITVAILIVVT VAFVQEYRSE KSLEELSKLV PPECHCVREG KLEHTLARDL VPGDTVCLSV GDRVPADLRL FEAVDLSIDE SSLTGETTPC SKVTAPQPAA TNGDLASRSN IAFMGTLVRC GKAKGVVIGT GENSEFGEVF KMMQAEEAPK TPLQKSMDLL GKQLSFYSFG IIGIIMLVGW LLGKDILEMF TISVSLAVAA IPEGLPIVVT VTLALGVMRM VKKRAIVKKL PIVETLGCCN VICSDKTGTL TKNEMTVTHI FTSDGLHAEV TGVGYNQFGE VIVDGDVVHG FYNPAVSRIV EAGCVCNDAV IRNNTLMGKP TEGALIALAM KMGLDGLQQD YIRKAEYPFS SEQKWMAVKC VHRTQQDRPE ICFMKGAYEQ VIKYCTTYQS KGQTLTLTQQ QRDVYQQEKA RMGSAGLRVL ALASGPELGQ LTFLGLVGII DPPRTGVKEA VTTLIASGVS IKMITGDSQE TAVAIASRLG LYSKTSQSVS GEEIDAMDVQ QLSQIVPKVA VFYRASPRHK MKIIKSLQKN GSVVAMTGDG VNDAVALKAA DIGVAMGQTG TDVCKEAADM ILVDDDFQTI MSAIEEGKGI YNNIKNFVRF QLSTSIAALT LISLATLMNF PNPLNAMQIL WINIIMDGPP AQSLGVEPVD KDVIRKPPRN WKDSILTKNL ILKILVSSII IVCGTLFVFW RELRDNVITP RDTTMTFTCF VFFDMFNALS SRSQTKSVFE IGLCSNRMFC YAVLGSIMGQ LLVIYFPPLQ KVFQTESLSI LDLLFLLGLT SSVCIVAEII KKVERSREKI QKHVSSTSSS FLEVWLWERS GQQLVEIHPH LETGLPLTED VSCV* | ||||||||||||||||
| Mutated AA sequence | MDSLLPPSRF SYFKKYPLHA IRRYLSTLRN QRAEEQVARF QKIPNGENET MIPVLTSKKA SELPVSEVAS ILQFKNPLIM LLLASAVISV LMHQFDDAVS ITVAILIVVT VAFVQEYRSE KSLEELSKLV PPECHCVREG KLEHTLARDL VPGDTVCLSV GDRVPADLRL FEAVDLSIDE SSLTGETTPC SKVTAPQPAA TNGDLASRSN IAFMGTLVRC GKAKGVVIGT GENSEFGEVF KMMQAEEAPK TPLQKSMDLL GKQLSFYSFG IIGIIMLVGW LLGKDILEMF TISVSLAVAA IPEGLPIVVT VTLALGVMRM VKKRAIVKKL PIVETLGCCN VICSDKTGTL TKNEMTVTHI FTSDGLHAEV TGVGYNQFGE VIVDGDVVHG FYNPAVSRIV EAGCVCNDAV IRNNTLMGKP TEGALIALAM KMGLDGLQQD YIRKAEYPFS SEQKWMAVKC VHRTQQDRPE ICFMKGAYEQ VIKYCTTYQS KGQTLTLTQQ QRDVYQQEKA RMGSAGLRVL ALASGPELGQ LTFLGLVGII DPPRTGVKEA VTTLIASGVS IKMITGDSQE TAVAIASRLG LYSKTSQSVS GEEIDAMDVQ QLSQIVPKVA VFYRASPRHK MKIIKSLQKN GSVVAMTGDG VNDAVALKAA DIGVAMGQTG TDVCKEAADM ILVDDDFQTI MSAIEEGKGI YSNIKNFVRF QLSTSIAALT LISLATLMNF PNPLNAMQIL WINIIMDGPP AQSLGVEPVD KDVIRKPPRN WKDSILTKNL ILKILVSSII IVCGTLFVFW RELRDNVITP RDTTMTFTCF VFFDMFNALS SRSQTKSVFE IGLCSNRMFC YAVLGSIMGQ LLVIYFPPLQ KVFQTESLSI LDLLFLLGLT SSVCIVAEII KKVERSREKI QKHVSSTSSS FLEVWLWERS GQQLVEIHPH LETGLPLTED VSCV* | ||||||||||||||||
| Position of stopcodon in wt / mu CDS | 2835 / 2835 | ||||||||||||||||
| Position (AA) of stopcodon in wt / mu AA sequence | 945 / 945 | ||||||||||||||||
| Position of stopcodon in wt / mu cDNA | 3061 / 3061 | ||||||||||||||||
| Position of start ATG in wt / mu cDNA | 227 / 227 | ||||||||||||||||
| Last intron/exon boundary | 2965 | ||||||||||||||||
| Theoretical NMD boundary in CDS | 2688 | ||||||||||||||||
| Length of CDS | 2835 | ||||||||||||||||
| Coding sequence (CDS) position | 2075 | ||||||||||||||||
| cDNA position | 2301 | ||||||||||||||||
| gDNA position | 145481 | ||||||||||||||||
| Chromosomal position | 130996075 | ||||||||||||||||
| Speed | 0.06 s | ||||||||||||||||
All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
| Analysed issue | Analysis result | ||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Variant | Chr3:130996075A>G (GRCh38) | ||||||||||||||||
| Gene symbol | ATP2C1 | ||||||||||||||||
| Gene constraints | LOEUF: 0.41, LOF (oe): 0.29, misssense (oe): 0.65, synonymous (oe): 0.90 (gnomAD) | ||||||||||||||||
| Ensembl transcript ID | ENST00000533801.6 | ||||||||||||||||
| Genbank transcript ID | NM_001001485 (by similarity) | ||||||||||||||||
| UniProt / AlphaMissense peptide | AT2C1_HUMAN | AlphaMissense: transcript, gene | ||||||||||||||||
| Variant type | Single base exchange | ||||||||||||||||
| Gene region | CDS | ||||||||||||||||
| DNA changes | c.2090A>G g.145481A>G | ||||||||||||||||
| AA changes |
| ||||||||||||||||
| Frameshift | No | ||||||||||||||||
| Length of protein | Normal | ||||||||||||||||
| Pathogenic variant (ClinVar) | Variant not listed in ClinVar as (likely) pathogenic. | ||||||||||||||||
| Variant DBs |
| ||||||||||||||||
| Protein conservation | |||||||||||||||||
| Protein features |
| ||||||||||||||||
| Phylogenetic conservation |
| ||||||||||||||||
| Splice sites | No abrogation of potential splice sites predicted by MaxEntScan. | ||||||||||||||||
| Distance from splice site | N/A | ||||||||||||||||
| Kozak consensus sequence altered? | No | ||||||||||||||||
| poly(A) signal | N/A | ||||||||||||||||
| AA sequence altered | Yes | ||||||||||||||||
| Chromosome | 3 | ||||||||||||||||
| Strand | 1 | ||||||||||||||||
| Original gDNA sequence snippet | AGAGGGTAAAGGGATTTATAATAACATTAAAAATTTCGTTA | ||||||||||||||||
| Altered gDNA sequence snippet | AGAGGGTAAAGGGATTTATAGTAACATTAAAAATTTCGTTA | ||||||||||||||||
| Original cDNA sequence snippet | AGAGGGTAAAGGGATTTATAATAACATTAAAAATTTCGTTA | ||||||||||||||||
| Altered cDNA sequence snippet | AGAGGGTAAAGGGATTTATAGTAACATTAAAAATTTCGTTA | ||||||||||||||||
| Wildtype AA sequence | MKVARFQKIP NGENETMIPV LTSKKASELP VSEVASILQA DLQNGLNKCE VSHRRAFHGW NEFDISEDEP LWKKYISQFK NPLIMLLLAS AVISVLMHQF DDAVSITVAI LIVVTVAFVQ EYRSEKSLEE LSKLVPPECH CVREGKLEHT LARDLVPGDT VCLSVGDRVP ADLRLFEAVD LSIDESSLTG ETTPCSKVTA PQPAATNGDL ASRSNIAFMG TLVRCGKAKG VVIGTGENSE FGEVFKMMQA EEAPKTPLQK SMDLLGKQLS FYSFGIIGII MLVGWLLGKD ILEMFTISVS LAVAAIPEGL PIVVTVTLAL GVMRMVKKRA IVKKLPIVET LGCCNVICSD KTGTLTKNEM TVTHIFTSDG LHAEVTGVGY NQFGEVIVDG DVVHGFYNPA VSRIVEAGCV CNDAVIRNNT LMGKPTEGAL IALAMKMGLD GLQQDYIRKA EYPFSSEQKW MAVKCVHRTQ QDRPEICFMK GAYEQVIKYC TTYQSKGQTL TLTQQQRDVY QQEKARMGSA GLRVLALASG PELGQLTFLG LVGIIDPPRT GVKEAVTTLI ASGVSIKMIT GDSQETAVAI ASRLGLYSKT SQSVSGEEID AMDVQQLSQI VPKVAVFYRA SPRHKMKIIK SLQKNGSVVA MTGDGVNDAV ALKAADIGVA MGQTGTDVCK EAADMILVDD DFQTIMSAIE EGKGIYNNIK NFVRFQLSTS IAALTLISLA TLMNFPNPLN AMQILWINII MDGPPAQSLG VEPVDKDVIR KPPRNWKDSI LTKNLILKIL VSSIIIVCGT LFVFWRELRD NVITPRDTTM TFTCFVFFDM FNALSSRSQT KSVFEIGLCS NRMFCYAVLG SIMGQLLVIY FPPLQKVFQT ESLSILGLAL GEEWTAAG* | ||||||||||||||||
| Mutated AA sequence | MKVARFQKIP NGENETMIPV LTSKKASELP VSEVASILQA DLQNGLNKCE VSHRRAFHGW NEFDISEDEP LWKKYISQFK NPLIMLLLAS AVISVLMHQF DDAVSITVAI LIVVTVAFVQ EYRSEKSLEE LSKLVPPECH CVREGKLEHT LARDLVPGDT VCLSVGDRVP ADLRLFEAVD LSIDESSLTG ETTPCSKVTA PQPAATNGDL ASRSNIAFMG TLVRCGKAKG VVIGTGENSE FGEVFKMMQA EEAPKTPLQK SMDLLGKQLS FYSFGIIGII MLVGWLLGKD ILEMFTISVS LAVAAIPEGL PIVVTVTLAL GVMRMVKKRA IVKKLPIVET LGCCNVICSD KTGTLTKNEM TVTHIFTSDG LHAEVTGVGY NQFGEVIVDG DVVHGFYNPA VSRIVEAGCV CNDAVIRNNT LMGKPTEGAL IALAMKMGLD GLQQDYIRKA EYPFSSEQKW MAVKCVHRTQ QDRPEICFMK GAYEQVIKYC TTYQSKGQTL TLTQQQRDVY QQEKARMGSA GLRVLALASG PELGQLTFLG LVGIIDPPRT GVKEAVTTLI ASGVSIKMIT GDSQETAVAI ASRLGLYSKT SQSVSGEEID AMDVQQLSQI VPKVAVFYRA SPRHKMKIIK SLQKNGSVVA MTGDGVNDAV ALKAADIGVA MGQTGTDVCK EAADMILVDD DFQTIMSAIE EGKGIYSNIK NFVRFQLSTS IAALTLISLA TLMNFPNPLN AMQILWINII MDGPPAQSLG VEPVDKDVIR KPPRNWKDSI LTKNLILKIL VSSIIIVCGT LFVFWRELRD NVITPRDTTM TFTCFVFFDM FNALSSRSQT KSVFEIGLCS NRMFCYAVLG SIMGQLLVIY FPPLQKVFQT ESLSILGLAL GEEWTAAG* | ||||||||||||||||
| Position of stopcodon in wt / mu CDS | 2667 / 2667 | ||||||||||||||||
| Position (AA) of stopcodon in wt / mu AA sequence | 889 / 889 | ||||||||||||||||
| Position of stopcodon in wt / mu cDNA | 3170 / 3170 | ||||||||||||||||
| Position of start ATG in wt / mu cDNA | 504 / 504 | ||||||||||||||||
| Last intron/exon boundary | 3132 | ||||||||||||||||
| Theoretical NMD boundary in CDS | 2578 | ||||||||||||||||
| Length of CDS | 2667 | ||||||||||||||||
| Coding sequence (CDS) position | 2090 | ||||||||||||||||
| cDNA position | 2593 | ||||||||||||||||
| gDNA position | 145481 | ||||||||||||||||
| Chromosomal position | 130996075 | ||||||||||||||||
| Speed | 0.04 s | ||||||||||||||||
All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
| Analysed issue | Analysis result | ||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Variant | Chr3:130996075A>G (GRCh38) | ||||||||||||||||
| Gene symbol | ATP2C1 | ||||||||||||||||
| Gene constraints | LOEUF: 0.41, LOF (oe): 0.29, misssense (oe): 0.65, synonymous (oe): 0.90 (gnomAD) | ||||||||||||||||
| Ensembl transcript ID | ENST00000328560.12 | ||||||||||||||||
| Genbank transcript ID | NM_001199185 (by similarity) | ||||||||||||||||
| UniProt / AlphaMissense peptide | AT2C1_HUMAN | AlphaMissense: transcript, gene | ||||||||||||||||
| Variant type | Single base exchange | ||||||||||||||||
| Gene region | CDS | ||||||||||||||||
| DNA changes | c.2090A>G g.145481A>G | ||||||||||||||||
| AA changes |
| ||||||||||||||||
| Frameshift | No | ||||||||||||||||
| Length of protein | Normal | ||||||||||||||||
| Pathogenic variant (ClinVar) | Variant not listed in ClinVar as (likely) pathogenic. | ||||||||||||||||
| Variant DBs |
| ||||||||||||||||
| Protein conservation | |||||||||||||||||
| Protein features |
| ||||||||||||||||
| Phylogenetic conservation |
| ||||||||||||||||
| Splice sites | No abrogation of potential splice sites predicted by MaxEntScan. | ||||||||||||||||
| Distance from splice site | N/A | ||||||||||||||||
| Kozak consensus sequence altered? | No | ||||||||||||||||
| poly(A) signal | N/A | ||||||||||||||||
| AA sequence altered | Yes | ||||||||||||||||
| Chromosome | 3 | ||||||||||||||||
| Strand | 1 | ||||||||||||||||
| Original gDNA sequence snippet | AGAGGGTAAAGGGATTTATAATAACATTAAAAATTTCGTTA | ||||||||||||||||
| Altered gDNA sequence snippet | AGAGGGTAAAGGGATTTATAGTAACATTAAAAATTTCGTTA | ||||||||||||||||
| Original cDNA sequence snippet | AGAGGGTAAAGGGATTTATAATAACATTAAAAATTTCGTTA | ||||||||||||||||
| Altered cDNA sequence snippet | AGAGGGTAAAGGGATTTATAGTAACATTAAAAATTTCGTTA | ||||||||||||||||
| Wildtype AA sequence | MKVARFQKIP NGENETMIPV LTSKKASELP VSEVASILQA DLQNGLNKCE VSHRRAFHGW NEFDISEDEP LWKKYISQFK NPLIMLLLAS AVISVLMHQF DDAVSITVAI LIVVTVAFVQ EYRSEKSLEE LSKLVPPECH CVREGKLEHT LARDLVPGDT VCLSVGDRVP ADLRLFEAVD LSIDESSLTG ETTPCSKVTA PQPAATNGDL ASRSNIAFMG TLVRCGKAKG VVIGTGENSE FGEVFKMMQA EEAPKTPLQK SMDLLGKQLS FYSFGIIGII MLVGWLLGKD ILEMFTISVS LAVAAIPEGL PIVVTVTLAL GVMRMVKKRA IVKKLPIVET LGCCNVICSD KTGTLTKNEM TVTHIFTSDG LHAEVTGVGY NQFGEVIVDG DVVHGFYNPA VSRIVEAGCV CNDAVIRNNT LMGKPTEGAL IALAMKMGLD GLQQDYIRKA EYPFSSEQKW MAVKCVHRTQ QDRPEICFMK GAYEQVIKYC TTYQSKGQTL TLTQQQRDVY QQEKARMGSA GLRVLALASG PELGQLTFLG LVGIIDPPRT GVKEAVTTLI ASGVSIKMIT GDSQETAVAI ASRLGLYSKT SQSVSGEEID AMDVQQLSQI VPKVAVFYRA SPRHKMKIIK SLQKNGSVVA MTGDGVNDAV ALKAADIGVA MGQTGTDVCK EAADMILVDD DFQTIMSAIE EGKGIYNNIK NFVRFQLSTS IAALTLISLA TLMNFPNPLN AMQILWINII MDGPPAQSLG VEPVDKDVIR KPPRNWKDSI LTKNLILKIL VSSIIIVCGT LFVFWRELRD NVITPRDTTM TFTCFVFFDM FNALSSRSQT KSVFEIGLCS NRMFCYAVLG SIMGQLLVIY FPPLQKVFQT ESLSILGLAL GEEWTAAG* | ||||||||||||||||
| Mutated AA sequence | MKVARFQKIP NGENETMIPV LTSKKASELP VSEVASILQA DLQNGLNKCE VSHRRAFHGW NEFDISEDEP LWKKYISQFK NPLIMLLLAS AVISVLMHQF DDAVSITVAI LIVVTVAFVQ EYRSEKSLEE LSKLVPPECH CVREGKLEHT LARDLVPGDT VCLSVGDRVP ADLRLFEAVD LSIDESSLTG ETTPCSKVTA PQPAATNGDL ASRSNIAFMG TLVRCGKAKG VVIGTGENSE FGEVFKMMQA EEAPKTPLQK SMDLLGKQLS FYSFGIIGII MLVGWLLGKD ILEMFTISVS LAVAAIPEGL PIVVTVTLAL GVMRMVKKRA IVKKLPIVET LGCCNVICSD KTGTLTKNEM TVTHIFTSDG LHAEVTGVGY NQFGEVIVDG DVVHGFYNPA VSRIVEAGCV CNDAVIRNNT LMGKPTEGAL IALAMKMGLD GLQQDYIRKA EYPFSSEQKW MAVKCVHRTQ QDRPEICFMK GAYEQVIKYC TTYQSKGQTL TLTQQQRDVY QQEKARMGSA GLRVLALASG PELGQLTFLG LVGIIDPPRT GVKEAVTTLI ASGVSIKMIT GDSQETAVAI ASRLGLYSKT SQSVSGEEID AMDVQQLSQI VPKVAVFYRA SPRHKMKIIK SLQKNGSVVA MTGDGVNDAV ALKAADIGVA MGQTGTDVCK EAADMILVDD DFQTIMSAIE EGKGIYSNIK NFVRFQLSTS IAALTLISLA TLMNFPNPLN AMQILWINII MDGPPAQSLG VEPVDKDVIR KPPRNWKDSI LTKNLILKIL VSSIIIVCGT LFVFWRELRD NVITPRDTTM TFTCFVFFDM FNALSSRSQT KSVFEIGLCS NRMFCYAVLG SIMGQLLVIY FPPLQKVFQT ESLSILGLAL GEEWTAAG* | ||||||||||||||||
| Position of stopcodon in wt / mu CDS | 2667 / 2667 | ||||||||||||||||
| Position (AA) of stopcodon in wt / mu AA sequence | 889 / 889 | ||||||||||||||||
| Position of stopcodon in wt / mu cDNA | 2989 / 2989 | ||||||||||||||||
| Position of start ATG in wt / mu cDNA | 323 / 323 | ||||||||||||||||
| Last intron/exon boundary | 2951 | ||||||||||||||||
| Theoretical NMD boundary in CDS | 2578 | ||||||||||||||||
| Length of CDS | 2667 | ||||||||||||||||
| Coding sequence (CDS) position | 2090 | ||||||||||||||||
| cDNA position | 2412 | ||||||||||||||||
| gDNA position | 145481 | ||||||||||||||||
| Chromosomal position | 130996075 | ||||||||||||||||
| Speed | 0.05 s | ||||||||||||||||
All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project