MutationT @ ster 2025

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Known disease mutation: ClinVar ID 594235 (pathogenic)
Protein features (might be) affected

Model: simple_aae
Tree vote: 99|1 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr16:56913365G>A (GRCh38)

Gene symbol

Gene constraints

LOEUF: 1.02, LOF (oe): 0.87, misssense (oe): 0.95, synonymous (oe): 0.98 ? (gnomAD)

Ensembl transcript ID

ENST00000438926.6

Genbank transcript ID

NM_000339 (by similarity)

UniProt / AlphaMissense peptide

S12A3_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.3053G>A
g.48159G>A

AA changes

AAE:	R1018Q	?
Score:	43

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Familial hypokalemia-hypomagnesemia

pathogenic

Variant DBs

dbSNP ID	rs370175770
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	34	34

Protein conservation

Species	Match	AA	Alignment
Human		1018	S	Q	D	L	R	P	P	V	I	L	I	R	G	N	Q	E	N	V	L	T	F	Y	C	Q
mutated	all conserved	1018	S	Q	D	L	R	P	P	V	I	L	I	Q	G	N
Ptroglodytes	no homologue
Mmulatta	no homologue
Fcatus	no homologue
Mmusculus	no homologue
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

Start (aa)	End (aa)	Feature	Details
1	1021	CHAIN		lost
600	1021	TOPO_DOM	Cytoplasmic	lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.586	0.997
	9.855	1
(flanking)	0.633	0.996

?

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

16

Strand

1

Original gDNA sequence snippet

ACCTCCAGTCATCCTGATCCGAGGAAACCAGGAAAACGTGC

Altered gDNA sequence snippet

ACCTCCAGTCATCCTGATCCAAGGAAACCAGGAAAACGTGC

Original cDNA sequence snippet

ACCTCCAGTCATCCTGATCCGAGGAAACCAGGAAAACGTGC

Altered cDNA sequence snippet

ACCTCCAGTCATCCTGATCCAAGGAAACCAGGAAAACGTGC

Wildtype AA sequence

MAELPTTETP GDATLCSGRF TISTLLSSDE PSPPAAYDSS HPSHLTHSST FCMRTFGYNT
IDVVPTYEHY ANSTQPGEPR KVRPTLADLH SFLKQEGRHL HALAFDSRPS HEMTDGLVEG
EAGTSSEKNP EEPVRFGWVK GVMIRCMLNI WGVILYLRLP WITAQAGIVL TWIIILLSVT
VTSITGLSIS AISTNGKVKS GGTYFLISRS LGPELGGSIG LIFAFANAVG VAMHTVGFAE
TVRDLLQEYG APIVDPINDI RIIAVVSVTV LLAISLAGME WESKAQVLFF LVIMVSFANY
LVGTLIPPSE DKASKGFFSY RADIFVQNLV PDWRGPDGTF FGMFSIFFPS ATGILAGANI
SGDLKDPAIA IPKGTLMAIF WTTISYLAIS ATIGSCVVRD ASGVLNDTVT PGWGACEGLA
CSYGWNFTEC TQQHSCHYGL INYYQTMSMV SGFAPLITAG IFGATLSSAL ACLVSAAKVF
QCLCEDQLYP LIGFFGKGYG KNKEPVRGYL LAYAIAVAFI IIAELNTIAP IISNFFLCSY
ALINFSCFHA SITNSPGWRP SFQYYNKWAA LFGAIISVVI MFLLTWWAAL IAIGVVLFLL
LYVIYKKPEV NWGSSVQAGS YNLALSYSVG LNEVEDHIKN YRPQCLVLTG PPNFRPALVD
FVGTFTRNLS LMICGHVLIG PHKQRMPELQ LIANGHTKWL NKRKIKAFYS DVIAEDLRRG
VQILMQAAGL GRMKPNILVV GFKKNWQSAH PATVEDYIGI LHDAFDFNYG VCVMRMREGL
NVSKMMQAHI NPVFDPAEDG KEASARGARP SVSGALDPKA LVKEEQATTI FQSEQGKKTI
DIYWLFDDGG LTLLIPYLLG RKRRWSKCKI RVFVGGQINR MDQERKAIIS LLSKFRLGFH
EVHILPDINQ NPRAEHTKRF EDMIAPFRLN DGFKDEATVN EMRRDCPWKI SDEEITKNRV
KSLRQVRLNE IVLDYSRDAA LIVITLPIGR KGKCPSSLYM AWLETLSQDL RPPVILIRGN
QENVLTFYCQ *

Mutated AA sequence

MAELPTTETP GDATLCSGRF TISTLLSSDE PSPPAAYDSS HPSHLTHSST FCMRTFGYNT
IDVVPTYEHY ANSTQPGEPR KVRPTLADLH SFLKQEGRHL HALAFDSRPS HEMTDGLVEG
EAGTSSEKNP EEPVRFGWVK GVMIRCMLNI WGVILYLRLP WITAQAGIVL TWIIILLSVT
VTSITGLSIS AISTNGKVKS GGTYFLISRS LGPELGGSIG LIFAFANAVG VAMHTVGFAE
TVRDLLQEYG APIVDPINDI RIIAVVSVTV LLAISLAGME WESKAQVLFF LVIMVSFANY
LVGTLIPPSE DKASKGFFSY RADIFVQNLV PDWRGPDGTF FGMFSIFFPS ATGILAGANI
SGDLKDPAIA IPKGTLMAIF WTTISYLAIS ATIGSCVVRD ASGVLNDTVT PGWGACEGLA
CSYGWNFTEC TQQHSCHYGL INYYQTMSMV SGFAPLITAG IFGATLSSAL ACLVSAAKVF
QCLCEDQLYP LIGFFGKGYG KNKEPVRGYL LAYAIAVAFI IIAELNTIAP IISNFFLCSY
ALINFSCFHA SITNSPGWRP SFQYYNKWAA LFGAIISVVI MFLLTWWAAL IAIGVVLFLL
LYVIYKKPEV NWGSSVQAGS YNLALSYSVG LNEVEDHIKN YRPQCLVLTG PPNFRPALVD
FVGTFTRNLS LMICGHVLIG PHKQRMPELQ LIANGHTKWL NKRKIKAFYS DVIAEDLRRG
VQILMQAAGL GRMKPNILVV GFKKNWQSAH PATVEDYIGI LHDAFDFNYG VCVMRMREGL
NVSKMMQAHI NPVFDPAEDG KEASARGARP SVSGALDPKA LVKEEQATTI FQSEQGKKTI
DIYWLFDDGG LTLLIPYLLG RKRRWSKCKI RVFVGGQINR MDQERKAIIS LLSKFRLGFH
EVHILPDINQ NPRAEHTKRF EDMIAPFRLN DGFKDEATVN EMRRDCPWKI SDEEITKNRV
KSLRQVRLNE IVLDYSRDAA LIVITLPIGR KGKCPSSLYM AWLETLSQDL RPPVILIQGN
QENVLTFYCQ *

Position of stopcodon in wt / mu CDS

3093 / 3093

Position (AA) of stopcodon in wt / mu AA sequence

1031 / 1031

Position of stopcodon in wt / mu cDNA

3122 / 3122

Position of start ATG in wt / mu cDNA

30 / 30

Last intron/exon boundary

2980

Theoretical NMD boundary in CDS

2900

Length of CDS

3093

Coding sequence (CDS) position

3053

cDNA position

3082

gDNA position

48159

Chromosomal position

56913365

Speed

0.10 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

MutationT@ster 2025

Variant:

16:56913365G>A_4_ENST00000563236

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Known disease mutation: ClinVar ID 594235 (pathogenic)
Protein features (might be) affected

Model: simple_aae
Tree vote: 99|1 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr16:56913365G>A (GRCh38)

Gene symbol

Gene constraints

LOEUF: 1.00, LOF (oe): 0.85, misssense (oe): 0.95, synonymous (oe): 0.98 ? (gnomAD)

Ensembl transcript ID

ENST00000563236.6

Genbank transcript ID

NM_001126108 (exact from MANE)

UniProt / AlphaMissense peptide

S12A3_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.3026G>A
g.48159G>A

AA changes

AAE:	R1009Q	?
Score:	43

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Familial hypokalemia-hypomagnesemia

pathogenic

Variant DBs

dbSNP ID	rs370175770
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	34	34

Protein conservation

Species	Match	AA	Alignment
Human		1009	S	Q	D	L	R	P	P	V	I	L	I	R	G	N	Q	E	N	V	L	T	F	Y	C	Q
mutated	all conserved	1009	S	Q	D	L	R	P	P	V	I	L	I	Q	G	N	Q	E	N	V	L	T	F	Y	C
Ptroglodytes	no alignment	n/a
Mmulatta	no alignment	n/a
Fcatus	no alignment	n/a
Mmusculus	no alignment	n/a
Ggallus	no alignment	n/a
Trubripes	no alignment	n/a
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no alignment	n/a

Protein features

Start (aa)	End (aa)	Feature	Details
1	1021	CHAIN		lost
600	1021	TOPO_DOM	Cytoplasmic	lost
1005	1009	STRAND		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.586	0.997
	9.855	1
(flanking)	0.633	0.996

?

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

16

Strand

1

Original gDNA sequence snippet

ACCTCCAGTCATCCTGATCCGAGGAAACCAGGAAAACGTGC

Altered gDNA sequence snippet

ACCTCCAGTCATCCTGATCCAAGGAAACCAGGAAAACGTGC

Original cDNA sequence snippet

ACCTCCAGTCATCCTGATCCGAGGAAACCAGGAAAACGTGC

Altered cDNA sequence snippet

ACCTCCAGTCATCCTGATCCAAGGAAACCAGGAAAACGTGC

Wildtype AA sequence

MAELPTTETP GDATLCSGRF TISTLLSSDE PSPPAAYDSS HPSHLTHSST FCMRTFGYNT
IDVVPTYEHY ANSTQPGEPR KVRPTLADLH SFLKQEGRHL HALAFDSRPS HEMTDGLVEG
EAGTSSEKNP EEPVRFGWVK GVMIRCMLNI WGVILYLRLP WITAQAGIVL TWIIILLSVT
VTSITGLSIS AISTNGKVKS GGTYFLISRS LGPELGGSIG LIFAFANAVG VAMHTVGFAE
TVRDLLQEYG APIVDPINDI RIIAVVSVTV LLAISLAGME WESKAQVLFF LVIMVSFANY
LVGTLIPPSE DKASKGFFSY RADIFVQNLV PDWRGPDGTF FGMFSIFFPS ATGILAGANI
SGDLKDPAIA IPKGTLMAIF WTTISYLAIS ATIGSCVVRD ASGVLNDTVT PGWGACEGLA
CSYGWNFTEC TQQHSCHYGL INYYQTMSMV SGFAPLITAG IFGATLSSAL ACLVSAAKVF
QCLCEDQLYP LIGFFGKGYG KNKEPVRGYL LAYAIAVAFI IIAELNTIAP IISNFFLCSY
ALINFSCFHA SITNSPGWRP SFQYYNKWAA LFGAIISVVI MFLLTWWAAL IAIGVVLFLL
LYVIYKKPEV NWGSSVQAGS YNLALSYSVG LNEVEDHIKN YRPQCLVLTG PPNFRPALVD
FVGTFTRNLS LMICGHVLIG PHKQRMPELQ LIANGHTKWL NKRKIKAFYS DVIAEDLRRG
VQILMQAAGL GRMKPNILVV GFKKNWQSAH PATVEDYIGI LHDAFDFNYG VCVMRMREGL
NVSKMMQAHI NPVFDPAEDG KEASARVDPK ALVKEEQATT IFQSEQGKKT IDIYWLFDDG
GLTLLIPYLL GRKRRWSKCK IRVFVGGQIN RMDQERKAII SLLSKFRLGF HEVHILPDIN
QNPRAEHTKR FEDMIAPFRL NDGFKDEATV NEMRRDCPWK ISDEEITKNR VKSLRQVRLN
EIVLDYSRDA ALIVITLPIG RKGKCPSSLY MAWLETLSQD LRPPVILIRG NQENVLTFYC
Q*

Mutated AA sequence

MAELPTTETP GDATLCSGRF TISTLLSSDE PSPPAAYDSS HPSHLTHSST FCMRTFGYNT
IDVVPTYEHY ANSTQPGEPR KVRPTLADLH SFLKQEGRHL HALAFDSRPS HEMTDGLVEG
EAGTSSEKNP EEPVRFGWVK GVMIRCMLNI WGVILYLRLP WITAQAGIVL TWIIILLSVT
VTSITGLSIS AISTNGKVKS GGTYFLISRS LGPELGGSIG LIFAFANAVG VAMHTVGFAE
TVRDLLQEYG APIVDPINDI RIIAVVSVTV LLAISLAGME WESKAQVLFF LVIMVSFANY
LVGTLIPPSE DKASKGFFSY RADIFVQNLV PDWRGPDGTF FGMFSIFFPS ATGILAGANI
SGDLKDPAIA IPKGTLMAIF WTTISYLAIS ATIGSCVVRD ASGVLNDTVT PGWGACEGLA
CSYGWNFTEC TQQHSCHYGL INYYQTMSMV SGFAPLITAG IFGATLSSAL ACLVSAAKVF
QCLCEDQLYP LIGFFGKGYG KNKEPVRGYL LAYAIAVAFI IIAELNTIAP IISNFFLCSY
ALINFSCFHA SITNSPGWRP SFQYYNKWAA LFGAIISVVI MFLLTWWAAL IAIGVVLFLL
LYVIYKKPEV NWGSSVQAGS YNLALSYSVG LNEVEDHIKN YRPQCLVLTG PPNFRPALVD
FVGTFTRNLS LMICGHVLIG PHKQRMPELQ LIANGHTKWL NKRKIKAFYS DVIAEDLRRG
VQILMQAAGL GRMKPNILVV GFKKNWQSAH PATVEDYIGI LHDAFDFNYG VCVMRMREGL
NVSKMMQAHI NPVFDPAEDG KEASARVDPK ALVKEEQATT IFQSEQGKKT IDIYWLFDDG
GLTLLIPYLL GRKRRWSKCK IRVFVGGQIN RMDQERKAII SLLSKFRLGF HEVHILPDIN
QNPRAEHTKR FEDMIAPFRL NDGFKDEATV NEMRRDCPWK ISDEEITKNR VKSLRQVRLN
EIVLDYSRDA ALIVITLPIG RKGKCPSSLY MAWLETLSQD LRPPVILIQG NQENVLTFYC
Q*

Position of stopcodon in wt / mu CDS

3066 / 3066

Position (AA) of stopcodon in wt / mu AA sequence

1022 / 1022

Position of stopcodon in wt / mu cDNA

3095 / 3095

Position of start ATG in wt / mu cDNA

30 / 30

Last intron/exon boundary

2953

Theoretical NMD boundary in CDS

2873

Length of CDS

3066

Coding sequence (CDS) position

3026

cDNA position

3055

gDNA position

48159

Chromosomal position

56913365

Speed

0.08 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

MutationT@ster 2025

Variant:

16:56913365G>A_2_ENST00000262502

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Known disease mutation: ClinVar ID 594235 (pathogenic)

Model: simple_aae
Tree vote: 100|0 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr16:56913365G>A (GRCh38)

Gene symbol

Gene constraints

LOEUF: 0.99, LOF (oe): 0.84, misssense (oe): 0.94, synonymous (oe): 0.98 ? (gnomAD)

Ensembl transcript ID

ENST00000262502.5

Genbank transcript ID

NM_001410896 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.3023G>A
g.48159G>A

AA changes

AAE:	R1008Q	?
Score:	43

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Familial hypokalemia-hypomagnesemia

pathogenic

Variant DBs

dbSNP ID	rs370175770
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	34	34

Protein conservation

Species	Match	AA	Alignment
Human		1008	S	Q	D	L	R	P	P	V	I	L	I	R	G	N	Q	E	N	V	L	T	F	Y	C	Q
mutated	all conserved	1008	S	Q	D	L	R	P	P	V	I	L	I	Q	G	N	Q	E	N	V	L	T	F	Y	C
Ptroglodytes	no homologue
Mmulatta	no homologue
Fcatus	no homologue
Mmusculus	no homologue
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.586	0.997
	9.855	1
(flanking)	0.633	0.996

?

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

16

Strand

1

Original gDNA sequence snippet

ACCTCCAGTCATCCTGATCCGAGGAAACCAGGAAAACGTGC

Altered gDNA sequence snippet

ACCTCCAGTCATCCTGATCCAAGGAAACCAGGAAAACGTGC

Original cDNA sequence snippet

ACCTCCAGTCATCCTGATCCGAGGAAACCAGGAAAACGTGC

Altered cDNA sequence snippet

ACCTCCAGTCATCCTGATCCAAGGAAACCAGGAAAACGTGC

Wildtype AA sequence

MAELPTTETP GDATLCSGRF TISTLLSSDE PSPPAAYDSS HPSHLTHSST FCMRTFGYNT
IDVVPTYEHY ANSTQPGEPR KVRPTLADLH SFLKEGRHLH ALAFDSRPSH EMTDGLVEGE
AGTSSEKNPE EPVRFGWVKG VMIRCMLNIW GVILYLRLPW ITAQAGIVLT WIIILLSVTV
TSITGLSISA ISTNGKVKSG GTYFLISRSL GPELGGSIGL IFAFANAVGV AMHTVGFAET
VRDLLQEYGA PIVDPINDIR IIAVVSVTVL LAISLAGMEW ESKAQVLFFL VIMVSFANYL
VGTLIPPSED KASKGFFSYR ADIFVQNLVP DWRGPDGTFF GMFSIFFPSA TGILAGANIS
GDLKDPAIAI PKGTLMAIFW TTISYLAISA TIGSCVVRDA SGVLNDTVTP GWGACEGLAC
SYGWNFTECT QQHSCHYGLI NYYQTMSMVS GFAPLITAGI FGATLSSALA CLVSAAKVFQ
CLCEDQLYPL IGFFGKGYGK NKEPVRGYLL AYAIAVAFII IAELNTIAPI ISNFFLCSYA
LINFSCFHAS ITNSPGWRPS FQYYNKWAAL FGAIISVVIM FLLTWWAALI AIGVVLFLLL
YVIYKKPEVN WGSSVQAGSY NLALSYSVGL NEVEDHIKNY RPQCLVLTGP PNFRPALVDF
VGTFTRNLSL MICGHVLIGP HKQRMPELQL IANGHTKWLN KRKIKAFYSD VIAEDLRRGV
QILMQAAGLG RMKPNILVVG FKKNWQSAHP ATVEDYIGIL HDAFDFNYGV CVMRMREGLN
VSKMMQAHIN PVFDPAEDGK EASARVDPKA LVKEEQATTI FQSEQGKKTI DIYWLFDDGG
LTLLIPYLLG RKRRWSKCKI RVFVGGQINR MDQERKAIIS LLSKFRLGFH EVHILPDINQ
NPRAEHTKRF EDMIAPFRLN DGFKDEATVN EMRRDCPWKI SDEEITKNRV KSLRQVRLNE
IVLDYSRDAA LIVITLPIGR KGKCPSSLYM AWLETLSQDL RPPVILIRGN QENVLTFYCQ
*

Mutated AA sequence

MAELPTTETP GDATLCSGRF TISTLLSSDE PSPPAAYDSS HPSHLTHSST FCMRTFGYNT
IDVVPTYEHY ANSTQPGEPR KVRPTLADLH SFLKEGRHLH ALAFDSRPSH EMTDGLVEGE
AGTSSEKNPE EPVRFGWVKG VMIRCMLNIW GVILYLRLPW ITAQAGIVLT WIIILLSVTV
TSITGLSISA ISTNGKVKSG GTYFLISRSL GPELGGSIGL IFAFANAVGV AMHTVGFAET
VRDLLQEYGA PIVDPINDIR IIAVVSVTVL LAISLAGMEW ESKAQVLFFL VIMVSFANYL
VGTLIPPSED KASKGFFSYR ADIFVQNLVP DWRGPDGTFF GMFSIFFPSA TGILAGANIS
GDLKDPAIAI PKGTLMAIFW TTISYLAISA TIGSCVVRDA SGVLNDTVTP GWGACEGLAC
SYGWNFTECT QQHSCHYGLI NYYQTMSMVS GFAPLITAGI FGATLSSALA CLVSAAKVFQ
CLCEDQLYPL IGFFGKGYGK NKEPVRGYLL AYAIAVAFII IAELNTIAPI ISNFFLCSYA
LINFSCFHAS ITNSPGWRPS FQYYNKWAAL FGAIISVVIM FLLTWWAALI AIGVVLFLLL
YVIYKKPEVN WGSSVQAGSY NLALSYSVGL NEVEDHIKNY RPQCLVLTGP PNFRPALVDF
VGTFTRNLSL MICGHVLIGP HKQRMPELQL IANGHTKWLN KRKIKAFYSD VIAEDLRRGV
QILMQAAGLG RMKPNILVVG FKKNWQSAHP ATVEDYIGIL HDAFDFNYGV CVMRMREGLN
VSKMMQAHIN PVFDPAEDGK EASARVDPKA LVKEEQATTI FQSEQGKKTI DIYWLFDDGG
LTLLIPYLLG RKRRWSKCKI RVFVGGQINR MDQERKAIIS LLSKFRLGFH EVHILPDINQ
NPRAEHTKRF EDMIAPFRLN DGFKDEATVN EMRRDCPWKI SDEEITKNRV KSLRQVRLNE
IVLDYSRDAA LIVITLPIGR KGKCPSSLYM AWLETLSQDL RPPVILIQGN QENVLTFYCQ
*

Position of stopcodon in wt / mu CDS

3063 / 3063

Position (AA) of stopcodon in wt / mu AA sequence

1021 / 1021

Position of stopcodon in wt / mu cDNA

3088 / 3088

Position of start ATG in wt / mu cDNA

26 / 26

Last intron/exon boundary

2946

Theoretical NMD boundary in CDS

2870

Length of CDS

3063

Coding sequence (CDS) position

3023

cDNA position

3048

gDNA position

48159

Chromosomal position

56913365

Speed

0.08 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

MutationT@ster 2025

Variant:

16:56913365G>A_1_ENST00000566786

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Known disease mutation: ClinVar ID 594235 (pathogenic)
Protein features (might be) affected

Model: simple_aae
Tree vote: 100|0 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr16:56913365G>A (GRCh38)

Gene symbol

Gene constraints

LOEUF: 1.01, LOF (oe): 0.86, misssense (oe): 0.95, synonymous (oe): 0.98 ? (gnomAD)

Ensembl transcript ID

ENST00000566786.5

Genbank transcript ID

NM_001126107 (by similarity)

UniProt / AlphaMissense peptide

S12A3_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.3050G>A
g.48159G>A

AA changes

AAE:	R1017Q	?
Score:	43

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Familial hypokalemia-hypomagnesemia

pathogenic

Variant DBs

dbSNP ID	rs370175770
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	34	34

Protein conservation

Species	Match	AA	Alignment
Human		1017	S	Q	D	L	R	P	P	V	I	L	I	R	G	N	Q	E	N	V	L	T	F	Y	C	Q
mutated	all conserved	1017	S	Q	D	L	R	P	P	V	I	L	I	Q	G	N	Q
Ptroglodytes	no homologue
Mmulatta	no homologue
Fcatus	no homologue
Mmusculus	no homologue
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

Start (aa)	End (aa)	Feature	Details
1	1021	CHAIN		lost
600	1021	TOPO_DOM	Cytoplasmic	lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.586	0.997
	9.855	1
(flanking)	0.633	0.996

?

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

16

Strand

1

Original gDNA sequence snippet

ACCTCCAGTCATCCTGATCCGAGGAAACCAGGAAAACGTGC

Altered gDNA sequence snippet

ACCTCCAGTCATCCTGATCCAAGGAAACCAGGAAAACGTGC

Original cDNA sequence snippet

ACCTCCAGTCATCCTGATCCGAGGAAACCAGGAAAACGTGC

Altered cDNA sequence snippet

ACCTCCAGTCATCCTGATCCAAGGAAACCAGGAAAACGTGC

Wildtype AA sequence

MAELPTTETP GDATLCSGRF TISTLLSSDE PSPPAAYDSS HPSHLTHSST FCMRTFGYNT
IDVVPTYEHY ANSTQPGEPR KVRPTLADLH SFLKEGRHLH ALAFDSRPSH EMTDGLVEGE
AGTSSEKNPE EPVRFGWVKG VMIRCMLNIW GVILYLRLPW ITAQAGIVLT WIIILLSVTV
TSITGLSISA ISTNGKVKSG GTYFLISRSL GPELGGSIGL IFAFANAVGV AMHTVGFAET
VRDLLQEYGA PIVDPINDIR IIAVVSVTVL LAISLAGMEW ESKAQVLFFL VIMVSFANYL
VGTLIPPSED KASKGFFSYR ADIFVQNLVP DWRGPDGTFF GMFSIFFPSA TGILAGANIS
GDLKDPAIAI PKGTLMAIFW TTISYLAISA TIGSCVVRDA SGVLNDTVTP GWGACEGLAC
SYGWNFTECT QQHSCHYGLI NYYQTMSMVS GFAPLITAGI FGATLSSALA CLVSAAKVFQ
CLCEDQLYPL IGFFGKGYGK NKEPVRGYLL AYAIAVAFII IAELNTIAPI ISNFFLCSYA
LINFSCFHAS ITNSPGWRPS FQYYNKWAAL FGAIISVVIM FLLTWWAALI AIGVVLFLLL
YVIYKKPEVN WGSSVQAGSY NLALSYSVGL NEVEDHIKNY RPQCLVLTGP PNFRPALVDF
VGTFTRNLSL MICGHVLIGP HKQRMPELQL IANGHTKWLN KRKIKAFYSD VIAEDLRRGV
QILMQAAGLG RMKPNILVVG FKKNWQSAHP ATVEDYIGIL HDAFDFNYGV CVMRMREGLN
VSKMMQAHIN PVFDPAEDGK EASARGARPS VSGALDPKAL VKEEQATTIF QSEQGKKTID
IYWLFDDGGL TLLIPYLLGR KRRWSKCKIR VFVGGQINRM DQERKAIISL LSKFRLGFHE
VHILPDINQN PRAEHTKRFE DMIAPFRLND GFKDEATVNE MRRDCPWKIS DEEITKNRVK
SLRQVRLNEI VLDYSRDAAL IVITLPIGRK GKCPSSLYMA WLETLSQDLR PPVILIRGNQ
ENVLTFYCQ*

Mutated AA sequence

MAELPTTETP GDATLCSGRF TISTLLSSDE PSPPAAYDSS HPSHLTHSST FCMRTFGYNT
IDVVPTYEHY ANSTQPGEPR KVRPTLADLH SFLKEGRHLH ALAFDSRPSH EMTDGLVEGE
AGTSSEKNPE EPVRFGWVKG VMIRCMLNIW GVILYLRLPW ITAQAGIVLT WIIILLSVTV
TSITGLSISA ISTNGKVKSG GTYFLISRSL GPELGGSIGL IFAFANAVGV AMHTVGFAET
VRDLLQEYGA PIVDPINDIR IIAVVSVTVL LAISLAGMEW ESKAQVLFFL VIMVSFANYL
VGTLIPPSED KASKGFFSYR ADIFVQNLVP DWRGPDGTFF GMFSIFFPSA TGILAGANIS
GDLKDPAIAI PKGTLMAIFW TTISYLAISA TIGSCVVRDA SGVLNDTVTP GWGACEGLAC
SYGWNFTECT QQHSCHYGLI NYYQTMSMVS GFAPLITAGI FGATLSSALA CLVSAAKVFQ
CLCEDQLYPL IGFFGKGYGK NKEPVRGYLL AYAIAVAFII IAELNTIAPI ISNFFLCSYA
LINFSCFHAS ITNSPGWRPS FQYYNKWAAL FGAIISVVIM FLLTWWAALI AIGVVLFLLL
YVIYKKPEVN WGSSVQAGSY NLALSYSVGL NEVEDHIKNY RPQCLVLTGP PNFRPALVDF
VGTFTRNLSL MICGHVLIGP HKQRMPELQL IANGHTKWLN KRKIKAFYSD VIAEDLRRGV
QILMQAAGLG RMKPNILVVG FKKNWQSAHP ATVEDYIGIL HDAFDFNYGV CVMRMREGLN
VSKMMQAHIN PVFDPAEDGK EASARGARPS VSGALDPKAL VKEEQATTIF QSEQGKKTID
IYWLFDDGGL TLLIPYLLGR KRRWSKCKIR VFVGGQINRM DQERKAIISL LSKFRLGFHE
VHILPDINQN PRAEHTKRFE DMIAPFRLND GFKDEATVNE MRRDCPWKIS DEEITKNRVK
SLRQVRLNEI VLDYSRDAAL IVITLPIGRK GKCPSSLYMA WLETLSQDLR PPVILIQGNQ
ENVLTFYCQ*

Position of stopcodon in wt / mu CDS

3090 / 3090

Position (AA) of stopcodon in wt / mu AA sequence

1030 / 1030

Position of stopcodon in wt / mu cDNA

3119 / 3119

Position of start ATG in wt / mu cDNA

30 / 30

Last intron/exon boundary

2977

Theoretical NMD boundary in CDS

2897

Length of CDS

3090

Coding sequence (CDS) position

3050

cDNA position

3079

gDNA position

48159

Chromosomal position

56913365

Speed

0.09 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