Results

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Input seems to be ok - now mapping the variant to the different transcripts...
Querying Taster for transcript #1: ENST00000413689
Querying Taster for transcript #2: ENST00000423572
Querying Taster for transcript #3: ENST00000455624
Querying Taster for transcript #4: ENST00000450102
Querying Taster for transcript #5: ENST00000449557
Querying Taster for transcript #6: ENST00000333535
Querying Taster for transcript #7: ENST00000327956
Querying Taster for transcript #8: ENST00000414099
MT speed 0.67 s - this script 3.162489 s

Transcript summary:

Permalink

Transcript	Gene symbol	Prediction	Tree vote	Model	Splice site change	Variant type	Protein length	Features at a glance
ENST00000413689(MANE Select)	SCN5A	Benign	28\|72	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Homozygous in gnomAD
ENST00000455624	SCN5A	Benign	28\|72	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Homozygous in gnomAD
ENST00000450102	SCN5A	Benign	28\|72	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Homozygous in gnomAD
ENST00000333535	SCN5A	Benign	28\|72	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Homozygous in gnomAD Protein features (might be) affected
ENST00000327956	SCN5A	Benign	28\|72	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Homozygous in gnomAD Protein features (might be) affected
ENST00000414099	SCN5A	Benign	28\|72	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Homozygous in gnomAD
ENST00000449557	SCN5A	Benign	29\|71	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Homozygous in gnomAD
ENST00000423572(MANE Select)	SCN5A	Benign	30\|70	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Homozygous in gnomAD Protein features (might be) affected

Variant:

3:38550521C>A_1_ENST00000413689

Back to summary table

Prediction:

BenignPermalink

Summary:

Amino acid sequence changed
Homozygous in gnomAD

Model: simple_aae
Tree vote: 28|72 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr3:38550521C>A (GRCh38)

Gene symbol

SCN5A

Gene constraints

LOEUF: 0.36, LOF (oe): 0.28, misssense (oe): 0.75, synonymous (oe): 0.91 ? (gnomAD)

Ensembl transcript ID

ENST00000413689.6

Genbank transcript ID

NM_001099404 (exact from MANE)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.5851G>T
g.99223G>T

AA changes

AAE:	V1951L	?
Score:	32

Frameshift

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs41315493
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	53	3115	3168

Protein conservation

Species	Match	AA	Alignment
Human		1951	D	A	P	E	R	E	G	L	I	A	Y	V	M	S	E	N	F	S	R	P	L	G	P	P
mutated	all conserved	1951	D	A	P	E	R	E	G	L	I	A	Y	L	M	S	E	N	F	S	R	P	L	G	P
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)	0.828	0.94
	0.927	0.931
(flanking)	1.413	0.912

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

Strand

-1

Original gDNA sequence snippet

GAGAGGGCCTCATCGCCTACGTGATGAGTGAGAACTTCTCC

Altered gDNA sequence snippet

GAGAGGGCCTCATCGCCTACTTGATGAGTGAGAACTTCTCC

Original cDNA sequence snippet

GAGAGGGCCTCATCGCCTACGTGATGAGTGAGAACTTCTCC

Altered cDNA sequence snippet

GAGAGGGCCTCATCGCCTACTTGATGAGTGAGAACTTCTCC

Wildtype AA sequence

MANFLLPRGT SSFRRFTRES LAAIEKRMAE KQARGSTTLQ ESREGLPEEE APRPQLDLQA
SKKLPDLYGN PPQELIGEPL EDLDPFYSTQ KTFIVLNKGK TIFRFSATNA LYVLSPFHPI
RRAAVKILVH SLFNMLIMCT ILTNCVFMAQ HDPPPWTKYV EYTFTAIYTF ESLVKILARG
FCLHAFTFLR DPWNWLDFSV IIMAYVSENI KLGNLSALRT FRVLRALKTI SVIPGLKTIV
GALIQSVKKL ADVMVLTVFC LSVFALIGLQ LFMGNLRHKC VRNFTALNGT NGSVEADGLV
WESLDLYLSD PENYLLKNGT SDVLLCGNSS DAGTCPEGYR CLKAGENPDH GYTSFDSFAW
AFLALFRLMT QDCWERLYQQ TLRSAGKIYM IFFMLVIFLG SFYLVNLILA VVAMAYEEQN
QATIAETEEK EKRFQEAMEM LKKEHEALTI RGVDTVSRSS LEMSPLAPVN SHERRSKRRK
RMSSGTEECG EDRLPKSDSE DGPRAMNHLS LTRGLSRTSM KPRSSRGSIF TFRRRDLGSE
ADFADDENST AGESESHHTS LLVPWPLRRT SAQGQPSPGT SAPGHALHGK KNSTVDCNGV
VSLLGAGDPE ATSPGSHLLR PVMLEHPPDT TTPSEEPGGP QMLTSQAPCV DGFEEPGARQ
RALSAVSVLT SALEELEESR HKCPPCWNRL AQRYLIWECC PLWMSIKQGV KLVVMDPFTD
LTITMCIVLN TLFMALEHYN MTSEFEEMLQ VGNLVFTGIF TAEMTFKIIA LDPYYYFQQG
WNIFDSIIVI LSLMELGLSR MSNLSVLRSF RLLRVFKLAK SWPTLNTLIK IIGNSVGALG
NLTLVLAIIV FIFAVVGMQL FGKNYSELRD SDSGLLPRWH MMDFFHAFLI IFRILCGEWI
ETMWDCMEVS GQSLCLLVFL LVMVIGNLVV LNLFLALLLS SFSADNLTAP DEDREMNNLQ
LALARIQRGL RFVKRTTWDF CCGLLRQRPQ KPAALAAQGQ LPSCIATPYS PPPPETEKVP
PTRKETRFEE GEQPGQGTPG DPEPVCVPIA VAESDTDDQE EDEENSLGTE EESSKQQESQ
PVSGGPEAPP DSRTWSQVSA TASSEAEASA SQADWRQQWK AEPQAPGCGE TPEDSCSEGS
TADMTNTAEL LEQIPDLGQD VKDPEDCFTE GCVRRCPCCA VDTTQAPGKV WWRLRKTCYH
IVEHSWFETF IIFMILLSSG ALAFEDIYLE ERKTIKVLLE YADKMFTYVF VLEMLLKWVA
YGFKKYFTNA WCWLDFLIVD VSLVSLVANT LGFAEMGPIK SLRTLRALRP LRALSRFEGM
RVVVNALVGA IPSIMNVLLV CLIFWLIFSI MGVNLFAGKF GRCINQTEGD LPLNYTIVNN
KSQCESLNLT GELYWTKVKV NFDNVGAGYL ALLQVATFKG WMDIMYAAVD SRGYEEQPQW
EYNLYMYIYF VIFIIFGSFF TLNLFIGVII DNFNQQKKKL GGQDIFMTEE QKKYYNAMKK
LGSKKPQKPI PRPLNKYQGF IFDIVTKQAF DVTIMFLICL NMVTMMVETD DQSPEKINIL
AKINLLFVAI FTGECIVKLA ALRHYYFTNS WNIFDFVVVI LSIVGTVLSD IIQKYFFSPT
LFRVIRLARI GRILRLIRGA KGIRTLLFAL MMSLPALFNI GLLLFLVMFI YSIFGMANFA
YVKWEAGIDD MFNFQTFANS MLCLFQITTS AGWDGLLSPI LNTGPPYCDP TLPNSNGSRG
DCGSPAVGIL FFTTYIIISF LIVVNMYIAI ILENFSVATE ESTEPLSEDD FDMFYEIWEK
FDPEATQFIE YSVLSDFADA LSEPLRIAKP NQISLINMDL PMVSGDRIHC MDILFAFTKR
VLGESGEMDA LKIQMEEKFM AANPSKISYE PITTTLRRKH EEVSAMVIQR AFRRHLLQRS
LKHASFLFRQ QAGSGLSEED APEREGLIAY VMSENFSRPL GPPSSSSISS TSFPPSYDSV
TRATSDNLQV RGSDYSHSED LADFPPSPDR DRESIV*

Mutated AA sequence

MANFLLPRGT SSFRRFTRES LAAIEKRMAE KQARGSTTLQ ESREGLPEEE APRPQLDLQA
SKKLPDLYGN PPQELIGEPL EDLDPFYSTQ KTFIVLNKGK TIFRFSATNA LYVLSPFHPI
RRAAVKILVH SLFNMLIMCT ILTNCVFMAQ HDPPPWTKYV EYTFTAIYTF ESLVKILARG
FCLHAFTFLR DPWNWLDFSV IIMAYVSENI KLGNLSALRT FRVLRALKTI SVIPGLKTIV
GALIQSVKKL ADVMVLTVFC LSVFALIGLQ LFMGNLRHKC VRNFTALNGT NGSVEADGLV
WESLDLYLSD PENYLLKNGT SDVLLCGNSS DAGTCPEGYR CLKAGENPDH GYTSFDSFAW
AFLALFRLMT QDCWERLYQQ TLRSAGKIYM IFFMLVIFLG SFYLVNLILA VVAMAYEEQN
QATIAETEEK EKRFQEAMEM LKKEHEALTI RGVDTVSRSS LEMSPLAPVN SHERRSKRRK
RMSSGTEECG EDRLPKSDSE DGPRAMNHLS LTRGLSRTSM KPRSSRGSIF TFRRRDLGSE
ADFADDENST AGESESHHTS LLVPWPLRRT SAQGQPSPGT SAPGHALHGK KNSTVDCNGV
VSLLGAGDPE ATSPGSHLLR PVMLEHPPDT TTPSEEPGGP QMLTSQAPCV DGFEEPGARQ
RALSAVSVLT SALEELEESR HKCPPCWNRL AQRYLIWECC PLWMSIKQGV KLVVMDPFTD
LTITMCIVLN TLFMALEHYN MTSEFEEMLQ VGNLVFTGIF TAEMTFKIIA LDPYYYFQQG
WNIFDSIIVI LSLMELGLSR MSNLSVLRSF RLLRVFKLAK SWPTLNTLIK IIGNSVGALG
NLTLVLAIIV FIFAVVGMQL FGKNYSELRD SDSGLLPRWH MMDFFHAFLI IFRILCGEWI
ETMWDCMEVS GQSLCLLVFL LVMVIGNLVV LNLFLALLLS SFSADNLTAP DEDREMNNLQ
LALARIQRGL RFVKRTTWDF CCGLLRQRPQ KPAALAAQGQ LPSCIATPYS PPPPETEKVP
PTRKETRFEE GEQPGQGTPG DPEPVCVPIA VAESDTDDQE EDEENSLGTE EESSKQQESQ
PVSGGPEAPP DSRTWSQVSA TASSEAEASA SQADWRQQWK AEPQAPGCGE TPEDSCSEGS
TADMTNTAEL LEQIPDLGQD VKDPEDCFTE GCVRRCPCCA VDTTQAPGKV WWRLRKTCYH
IVEHSWFETF IIFMILLSSG ALAFEDIYLE ERKTIKVLLE YADKMFTYVF VLEMLLKWVA
YGFKKYFTNA WCWLDFLIVD VSLVSLVANT LGFAEMGPIK SLRTLRALRP LRALSRFEGM
RVVVNALVGA IPSIMNVLLV CLIFWLIFSI MGVNLFAGKF GRCINQTEGD LPLNYTIVNN
KSQCESLNLT GELYWTKVKV NFDNVGAGYL ALLQVATFKG WMDIMYAAVD SRGYEEQPQW
EYNLYMYIYF VIFIIFGSFF TLNLFIGVII DNFNQQKKKL GGQDIFMTEE QKKYYNAMKK
LGSKKPQKPI PRPLNKYQGF IFDIVTKQAF DVTIMFLICL NMVTMMVETD DQSPEKINIL
AKINLLFVAI FTGECIVKLA ALRHYYFTNS WNIFDFVVVI LSIVGTVLSD IIQKYFFSPT
LFRVIRLARI GRILRLIRGA KGIRTLLFAL MMSLPALFNI GLLLFLVMFI YSIFGMANFA
YVKWEAGIDD MFNFQTFANS MLCLFQITTS AGWDGLLSPI LNTGPPYCDP TLPNSNGSRG
DCGSPAVGIL FFTTYIIISF LIVVNMYIAI ILENFSVATE ESTEPLSEDD FDMFYEIWEK
FDPEATQFIE YSVLSDFADA LSEPLRIAKP NQISLINMDL PMVSGDRIHC MDILFAFTKR
VLGESGEMDA LKIQMEEKFM AANPSKISYE PITTTLRRKH EEVSAMVIQR AFRRHLLQRS
LKHASFLFRQ QAGSGLSEED APEREGLIAY LMSENFSRPL GPPSSSSISS TSFPPSYDSV
TRATSDNLQV RGSDYSHSED LADFPPSPDR DRESIV*

Position of stopcodon in wt / mu CDS

6051 / 6051

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

2017 / 2017

Position of stopcodon in wt / mu cDNA

6260 / 6260

Position of start ATG in wt / mu cDNA

210 / 210

Last intron/exon boundary

5022

Theoretical NMD boundary in CDS

4762

Length of CDS

6051

Coding sequence (CDS) position

5851

cDNA position

6060

gDNA position

99223

Chromosomal position

38550521

Speed

0.13 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

Back to summary table

Variant:

3:38550521C>A_3_ENST00000455624

Back to summary table

Prediction:

BenignPermalink

Summary:

Amino acid sequence changed
Homozygous in gnomAD

Model: simple_aae
Tree vote: 28|72 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr3:38550521C>A (GRCh38)

Gene symbol

SCN5A

Gene constraints

LOEUF: 0.36, LOF (oe): 0.28, misssense (oe): 0.74, synonymous (oe): 0.91 ? (gnomAD)

Ensembl transcript ID

ENST00000455624.6

Genbank transcript ID

NM_001160160 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.5752G>T
g.99223G>T

AA changes

AAE:	V1918L	?
Score:	32

Frameshift

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs41315493
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	53	3115	3168

Protein conservation

Species	Match	AA	Alignment
Human		1918	D	A	P	E	R	E	G	L	I	A	Y	V	M	S	E	N	F	S	R	P	L	G	P	P
mutated	all conserved	1918	D	A	P	E	R	E	G	L	I	A	Y	L	M	S
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)	0.828	0.94
	0.927	0.931
(flanking)	1.413	0.912

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

Strand

-1

Original gDNA sequence snippet

GAGAGGGCCTCATCGCCTACGTGATGAGTGAGAACTTCTCC

Altered gDNA sequence snippet

GAGAGGGCCTCATCGCCTACTTGATGAGTGAGAACTTCTCC

Original cDNA sequence snippet

GAGAGGGCCTCATCGCCTACGTGATGAGTGAGAACTTCTCC

Altered cDNA sequence snippet

GAGAGGGCCTCATCGCCTACTTGATGAGTGAGAACTTCTCC

Wildtype AA sequence

MANFLLPRGT SSFRRFTRES LAAIEKRMAE KQARGSTTLQ ESREGLPEEE APRPQLDLQA
SKKLPDLYGN PPQELIGEPL EDLDPFYSTQ KTFIVLNKGK TIFRFSATNA LYVLSPFHPI
RRAAVKILVH SLFNMLIMCT ILTNCVFMAQ HDPPPWTKYV EYTFTAIYTF ESLVKILARG
FCLHAFTFLR DPWNWLDFSV IIMAYVSENI KLGNLSALRT FRVLRALKTI SVIPGLKTIV
GALIQSVKKL ADVMVLTVFC LSVFALIGLQ LFMGNLRHKC VRNFTALNGT NGSVEADGLV
WESLDLYLSD PENYLLKNGT SDVLLCGNSS DAGTCPEGYR CLKAGENPDH GYTSFDSFAW
AFLALFRLMT QDCWERLYQQ TLRSAGKIYM IFFMLVIFLG SFYLVNLILA VVAMAYEEQN
QATIAETEEK EKRFQEAMEM LKKEHEALTI RGVDTVSRSS LEMSPLAPVN SHERRSKRRK
RMSSGTEECG EDRLPKSDSE DGPRAMNHLS LTRGLSRTSM KPRSSRGSIF TFRRRDLGSE
ADFADDENST AGESESHHTS LLVPWPLRRT SAQGQPSPGT SAPGHALHGK KNSTVDCNGV
VSLLGAGDPE ATSPGSHLLR PVMLEHPPDT TTPSEEPGGP QMLTSQAPCV DGFEEPGARQ
RALSAVSVLT SALEELEESR HKCPPCWNRL AQRYLIWECC PLWMSIKQGV KLVVMDPFTD
LTITMCIVLN TLFMALEHYN MTSEFEEMLQ VGNLVFTGIF TAEMTFKIIA LDPYYYFQQG
WNIFDSIIVI LSLMELGLSR MSNLSVLRSF RLLRVFKLAK SWPTLNTLIK IIGNSVGALG
NLTLVLAIIV FIFAVVGMQL FGKNYSELRD SDSGLLPRWH MMDFFHAFLI IFRILCGEWI
ETMWDCMEVS GQSLCLLVFL LVMVIGNLVV LNLFLALLLS SFSADNLTAP DEDREMNNLQ
LALARIQRGL RFVKRTTWDF CCGLLRQRPQ KPAALAAQGQ LPSCIATPYS PPPPETEKVP
PTRKETRFEE GEQPGQGTPG DPEPVCVPIA VAESDTDDQE EDEENSLGTE EESSKQESQP
VSGGPEAPPD SRTWSQVSAT ASSEAEASAS QADWRQQWKA EPQAPGCGET PEDSCSEGST
ADMTNTAELL EQIPDLGQDV KDPEDCFTEG CVRRCPCCAV DTTQAPGKVW WRLRKTCYHI
VEHSWFETFI IFMILLSSGA LAFEDIYLEE RKTIKVLLEY ADKMFTYVFV LEMLLKWVAY
GFKKYFTNAW CWLDFLIVDV SLVSLVANTL GFAEMGPIKS LRTLRALRPL RALSRFEGMR
VVVNALVGAI PSIMNVLLVC LIFWLIFSIM GVNLFAGKFG RCINQTEGDL PLNYTIVNNK
SQCESLNLTG ELYWTKVKVN FDNVGAGYLA LLQVATFKGW MDIMYAAVDS RGYEEQPQWE
YNLYMYIYFV IFIIFGSFFT LNLFIGVIID NFNQQKKKLG GQDIFMTEEQ KKYYNAMKKL
GSKKPQKPIP RPLNKYQGFI FDIVTKQAFD VTIMFLICLN MVTMMVETDD QSPEKINILA
KINLLFVAIF TGTVLSDIIQ KYFFSPTLFR VIRLARIGRI LRLIRGAKGI RTLLFALMMS
LPALFNIGLL LFLVMFIYSI FGMANFAYVK WEAGIDDMFN FQTFANSMLC LFQITTSAGW
DGLLSPILNT GPPYCDPTLP NSNGSRGDCG SPAVGILFFT TYIIISFLIV VNMYIAIILE
NFSVATEEST EPLSEDDFDM FYEIWEKFDP EATQFIEYSV LSDFADALSE PLRIAKPNQI
SLINMDLPMV SGDRIHCMDI LFAFTKRVLG ESGEMDALKI QMEEKFMAAN PSKISYEPIT
TTLRRKHEEV SAMVIQRAFR RHLLQRSLKH ASFLFRQQAG SGLSEEDAPE REGLIAYVMS
ENFSRPLGPP SSSSISSTSF PPSYDSVTRA TSDNLQVRGS DYSHSEDLAD FPPSPDRDRE
SIV*

Mutated AA sequence

MANFLLPRGT SSFRRFTRES LAAIEKRMAE KQARGSTTLQ ESREGLPEEE APRPQLDLQA
SKKLPDLYGN PPQELIGEPL EDLDPFYSTQ KTFIVLNKGK TIFRFSATNA LYVLSPFHPI
RRAAVKILVH SLFNMLIMCT ILTNCVFMAQ HDPPPWTKYV EYTFTAIYTF ESLVKILARG
FCLHAFTFLR DPWNWLDFSV IIMAYVSENI KLGNLSALRT FRVLRALKTI SVIPGLKTIV
GALIQSVKKL ADVMVLTVFC LSVFALIGLQ LFMGNLRHKC VRNFTALNGT NGSVEADGLV
WESLDLYLSD PENYLLKNGT SDVLLCGNSS DAGTCPEGYR CLKAGENPDH GYTSFDSFAW
AFLALFRLMT QDCWERLYQQ TLRSAGKIYM IFFMLVIFLG SFYLVNLILA VVAMAYEEQN
QATIAETEEK EKRFQEAMEM LKKEHEALTI RGVDTVSRSS LEMSPLAPVN SHERRSKRRK
RMSSGTEECG EDRLPKSDSE DGPRAMNHLS LTRGLSRTSM KPRSSRGSIF TFRRRDLGSE
ADFADDENST AGESESHHTS LLVPWPLRRT SAQGQPSPGT SAPGHALHGK KNSTVDCNGV
VSLLGAGDPE ATSPGSHLLR PVMLEHPPDT TTPSEEPGGP QMLTSQAPCV DGFEEPGARQ
RALSAVSVLT SALEELEESR HKCPPCWNRL AQRYLIWECC PLWMSIKQGV KLVVMDPFTD
LTITMCIVLN TLFMALEHYN MTSEFEEMLQ VGNLVFTGIF TAEMTFKIIA LDPYYYFQQG
WNIFDSIIVI LSLMELGLSR MSNLSVLRSF RLLRVFKLAK SWPTLNTLIK IIGNSVGALG
NLTLVLAIIV FIFAVVGMQL FGKNYSELRD SDSGLLPRWH MMDFFHAFLI IFRILCGEWI
ETMWDCMEVS GQSLCLLVFL LVMVIGNLVV LNLFLALLLS SFSADNLTAP DEDREMNNLQ
LALARIQRGL RFVKRTTWDF CCGLLRQRPQ KPAALAAQGQ LPSCIATPYS PPPPETEKVP
PTRKETRFEE GEQPGQGTPG DPEPVCVPIA VAESDTDDQE EDEENSLGTE EESSKQESQP
VSGGPEAPPD SRTWSQVSAT ASSEAEASAS QADWRQQWKA EPQAPGCGET PEDSCSEGST
ADMTNTAELL EQIPDLGQDV KDPEDCFTEG CVRRCPCCAV DTTQAPGKVW WRLRKTCYHI
VEHSWFETFI IFMILLSSGA LAFEDIYLEE RKTIKVLLEY ADKMFTYVFV LEMLLKWVAY
GFKKYFTNAW CWLDFLIVDV SLVSLVANTL GFAEMGPIKS LRTLRALRPL RALSRFEGMR
VVVNALVGAI PSIMNVLLVC LIFWLIFSIM GVNLFAGKFG RCINQTEGDL PLNYTIVNNK
SQCESLNLTG ELYWTKVKVN FDNVGAGYLA LLQVATFKGW MDIMYAAVDS RGYEEQPQWE
YNLYMYIYFV IFIIFGSFFT LNLFIGVIID NFNQQKKKLG GQDIFMTEEQ KKYYNAMKKL
GSKKPQKPIP RPLNKYQGFI FDIVTKQAFD VTIMFLICLN MVTMMVETDD QSPEKINILA
KINLLFVAIF TGTVLSDIIQ KYFFSPTLFR VIRLARIGRI LRLIRGAKGI RTLLFALMMS
LPALFNIGLL LFLVMFIYSI FGMANFAYVK WEAGIDDMFN FQTFANSMLC LFQITTSAGW
DGLLSPILNT GPPYCDPTLP NSNGSRGDCG SPAVGILFFT TYIIISFLIV VNMYIAIILE
NFSVATEEST EPLSEDDFDM FYEIWEKFDP EATQFIEYSV LSDFADALSE PLRIAKPNQI
SLINMDLPMV SGDRIHCMDI LFAFTKRVLG ESGEMDALKI QMEEKFMAAN PSKISYEPIT
TTLRRKHEEV SAMVIQRAFR RHLLQRSLKH ASFLFRQQAG SGLSEEDAPE REGLIAYLMS
ENFSRPLGPP SSSSISSTSF PPSYDSVTRA TSDNLQVRGS DYSHSEDLAD FPPSPDRDRE
SIV*

Position of stopcodon in wt / mu CDS

5952 / 5952

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

1984 / 1984

Position of stopcodon in wt / mu cDNA

5977 / 5977

Position of start ATG in wt / mu cDNA

26 / 26

Last intron/exon boundary

4739

Theoretical NMD boundary in CDS

4663

Length of CDS

5952

Coding sequence (CDS) position

5752

cDNA position

5777

gDNA position

99223

Chromosomal position

38550521

Speed

0.04 s

Back to summary table

Variant:

3:38550521C>A_4_ENST00000450102

Back to summary table

Prediction:

BenignPermalink

Summary:

Amino acid sequence changed
Homozygous in gnomAD

Model: simple_aae
Tree vote: 28|72 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr3:38550521C>A (GRCh38)

Gene symbol

SCN5A

Gene constraints

LOEUF: 0.35, LOF (oe): 0.27, misssense (oe): 0.74, synonymous (oe): 0.91 ? (gnomAD)

Ensembl transcript ID

ENST00000450102.6

Genbank transcript ID

NM_001160161 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.5689G>T
g.99223G>T

AA changes

AAE:	V1897L	?
Score:	32

Frameshift

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs41315493
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	53	3115	3168

Protein conservation

Species	Match	AA	Alignment
Human		1897	D	A	P	E	R	E	G	L	I	A	Y	V	M	S	E	N	F	S	R	P	L	G	P	P
mutated	all conserved	1897	D	A	P	E	R	E	G	L	I	A	Y	L	M	S	E	N	F	S	R	P	L	G	P
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)	0.828	0.94
	0.927	0.931
(flanking)	1.413	0.912

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

Strand

-1

Original gDNA sequence snippet

GAGAGGGCCTCATCGCCTACGTGATGAGTGAGAACTTCTCC

Altered gDNA sequence snippet

GAGAGGGCCTCATCGCCTACTTGATGAGTGAGAACTTCTCC

Original cDNA sequence snippet

GAGAGGGCCTCATCGCCTACGTGATGAGTGAGAACTTCTCC

Altered cDNA sequence snippet

GAGAGGGCCTCATCGCCTACTTGATGAGTGAGAACTTCTCC

Wildtype AA sequence

MANFLLPRGT SSFRRFTRES LAAIEKRMAE KQARGSTTLQ ESREGLPEEE APRPQLDLQA
SKKLPDLYGN PPQELIGEPL EDLDPFYSTQ KTFIVLNKGK TIFRFSATNA LYVLSPFHPI
RRAAVKILVH SLFNMLIMCT ILTNCVFMAQ HDPPPWTKYV EYTFTAIYTF ESLVKILARG
FCLHAFTFLR DPWNWLDFSV IIMAYVSENI KLGNLSALRT FRVLRALKTI SVIPGLKTIV
GALIQSVKKL ADVMVLTVFC LSVFALIGLQ LFMGNLRHKC VRNFTALNGT NGSVEADGLV
WESLDLYLSD PENYLLKNGT SDVLLCGNSS DAGTCPEGYR CLKAGENPDH GYTSFDSFAW
AFLALFRLMT QDCWERLYQQ TLRSAGKIYM IFFMLVIFLG SFYLVNLILA VVAMAYEEQN
QATIAETEEK EKRFQEAMEM LKKEHEALTI RGVDTVSRSS LEMSPLAPVN SHERRSKRRK
RMSSGTEECG EDRLPKSDSE DGPRAMNHLS LTRGLSRTSM KPRSSRGSIF TFRRRDLGSE
ADFADDENST AGESESHHTS LLVPWPLRRT SAQGQPSPGT SAPGHALHGK KNSTVDCNGV
VSLLGAGDPE ATSPGSHLLR PVMLEHPPDT TTPSEEPGGP QMLTSQAPCV DGFEEPGARQ
RALSAVSVLT SALEELEESR HKCPPCWNRL AQRYLIWECC PLWMSIKQGV KLVVMDPFTD
LTITMCIVLN TLFMALEHYN MTSEFEEMLQ VGNLVFTGIF TAEMTFKIIA LDPYYYFQQG
WNIFDSIIVI LSLMELGLSR MSNLSVLRSF RLLRVFKLAK SWPTLNTLIK IIGNSVGALG
NLTLVLAIIV FIFAVVGMQL FGKNYSELRD SDSGLLPRWH MMDFFHAFLI IFRILCGEWI
ETMWDCMEVS GQSLCLLVFL LVMVIGNLVV LNLFLALLLS SFSADNLTAP DEDREMNNLQ
LALARIQRGL RFVKRTTWDF CCGLLRQRPQ KPAALAAQGQ LPSCIATPYS PPPPETEKVP
PTRKETRFEE GEQPGQGTPG DPEPVCVPIA VAESDTDDQE EDEENSLGTE EESSKQTPED
SCSEGSTADM TNTAELLEQI PDLGQDVKDP EDCFTEGCVR RCPCCAVDTT QAPGKVWWRL
RKTCYHIVEH SWFETFIIFM ILLSSGALAF EDIYLEERKT IKVLLEYADK MFTYVFVLEM
LLKWVAYGFK KYFTNAWCWL DFLIVDVSLV SLVANTLGFA EMGPIKSLRT LRALRPLRAL
SRFEGMRVVV NALVGAIPSI MNVLLVCLIF WLIFSIMGVN LFAGKFGRCI NQTEGDLPLN
YTIVNNKSQC ESLNLTGELY WTKVKVNFDN VGAGYLALLQ VATFKGWMDI MYAAVDSRGY
EEQPQWEYNL YMYIYFVIFI IFGSFFTLNL FIGVIIDNFN QQKKKLGGQD IFMTEEQKKY
YNAMKKLGSK KPQKPIPRPL NKYQGFIFDI VTKQAFDVTI MFLICLNMVT MMVETDDQSP
EKINILAKIN LLFVAIFTGE CIVKLAALRH YYFTNSWNIF DFVVVILSIV GTVLSDIIQK
YFFSPTLFRV IRLARIGRIL RLIRGAKGIR TLLFALMMSL PALFNIGLLL FLVMFIYSIF
GMANFAYVKW EAGIDDMFNF QTFANSMLCL FQITTSAGWD GLLSPILNTG PPYCDPTLPN
SNGSRGDCGS PAVGILFFTT YIIISFLIVV NMYIAIILEN FSVATEESTE PLSEDDFDMF
YEIWEKFDPE ATQFIEYSVL SDFADALSEP LRIAKPNQIS LINMDLPMVS GDRIHCMDIL
FAFTKRVLGE SGEMDALKIQ MEEKFMAANP SKISYEPITT TLRRKHEEVS AMVIQRAFRR
HLLQRSLKHA SFLFRQQAGS GLSEEDAPER EGLIAYVMSE NFSRPLGPPS SSSISSTSFP
PSYDSVTRAT SDNLQVRGSD YSHSEDLADF PPSPDRDRES IV*

Mutated AA sequence

MANFLLPRGT SSFRRFTRES LAAIEKRMAE KQARGSTTLQ ESREGLPEEE APRPQLDLQA
SKKLPDLYGN PPQELIGEPL EDLDPFYSTQ KTFIVLNKGK TIFRFSATNA LYVLSPFHPI
RRAAVKILVH SLFNMLIMCT ILTNCVFMAQ HDPPPWTKYV EYTFTAIYTF ESLVKILARG
FCLHAFTFLR DPWNWLDFSV IIMAYVSENI KLGNLSALRT FRVLRALKTI SVIPGLKTIV
GALIQSVKKL ADVMVLTVFC LSVFALIGLQ LFMGNLRHKC VRNFTALNGT NGSVEADGLV
WESLDLYLSD PENYLLKNGT SDVLLCGNSS DAGTCPEGYR CLKAGENPDH GYTSFDSFAW
AFLALFRLMT QDCWERLYQQ TLRSAGKIYM IFFMLVIFLG SFYLVNLILA VVAMAYEEQN
QATIAETEEK EKRFQEAMEM LKKEHEALTI RGVDTVSRSS LEMSPLAPVN SHERRSKRRK
RMSSGTEECG EDRLPKSDSE DGPRAMNHLS LTRGLSRTSM KPRSSRGSIF TFRRRDLGSE
ADFADDENST AGESESHHTS LLVPWPLRRT SAQGQPSPGT SAPGHALHGK KNSTVDCNGV
VSLLGAGDPE ATSPGSHLLR PVMLEHPPDT TTPSEEPGGP QMLTSQAPCV DGFEEPGARQ
RALSAVSVLT SALEELEESR HKCPPCWNRL AQRYLIWECC PLWMSIKQGV KLVVMDPFTD
LTITMCIVLN TLFMALEHYN MTSEFEEMLQ VGNLVFTGIF TAEMTFKIIA LDPYYYFQQG
WNIFDSIIVI LSLMELGLSR MSNLSVLRSF RLLRVFKLAK SWPTLNTLIK IIGNSVGALG
NLTLVLAIIV FIFAVVGMQL FGKNYSELRD SDSGLLPRWH MMDFFHAFLI IFRILCGEWI
ETMWDCMEVS GQSLCLLVFL LVMVIGNLVV LNLFLALLLS SFSADNLTAP DEDREMNNLQ
LALARIQRGL RFVKRTTWDF CCGLLRQRPQ KPAALAAQGQ LPSCIATPYS PPPPETEKVP
PTRKETRFEE GEQPGQGTPG DPEPVCVPIA VAESDTDDQE EDEENSLGTE EESSKQTPED
SCSEGSTADM TNTAELLEQI PDLGQDVKDP EDCFTEGCVR RCPCCAVDTT QAPGKVWWRL
RKTCYHIVEH SWFETFIIFM ILLSSGALAF EDIYLEERKT IKVLLEYADK MFTYVFVLEM
LLKWVAYGFK KYFTNAWCWL DFLIVDVSLV SLVANTLGFA EMGPIKSLRT LRALRPLRAL
SRFEGMRVVV NALVGAIPSI MNVLLVCLIF WLIFSIMGVN LFAGKFGRCI NQTEGDLPLN
YTIVNNKSQC ESLNLTGELY WTKVKVNFDN VGAGYLALLQ VATFKGWMDI MYAAVDSRGY
EEQPQWEYNL YMYIYFVIFI IFGSFFTLNL FIGVIIDNFN QQKKKLGGQD IFMTEEQKKY
YNAMKKLGSK KPQKPIPRPL NKYQGFIFDI VTKQAFDVTI MFLICLNMVT MMVETDDQSP
EKINILAKIN LLFVAIFTGE CIVKLAALRH YYFTNSWNIF DFVVVILSIV GTVLSDIIQK
YFFSPTLFRV IRLARIGRIL RLIRGAKGIR TLLFALMMSL PALFNIGLLL FLVMFIYSIF
GMANFAYVKW EAGIDDMFNF QTFANSMLCL FQITTSAGWD GLLSPILNTG PPYCDPTLPN
SNGSRGDCGS PAVGILFFTT YIIISFLIVV NMYIAIILEN FSVATEESTE PLSEDDFDMF
YEIWEKFDPE ATQFIEYSVL SDFADALSEP LRIAKPNQIS LINMDLPMVS GDRIHCMDIL
FAFTKRVLGE SGEMDALKIQ MEEKFMAANP SKISYEPITT TLRRKHEEVS AMVIQRAFRR
HLLQRSLKHA SFLFRQQAGS GLSEEDAPER EGLIAYLMSE NFSRPLGPPS SSSISSTSFP
PSYDSVTRAT SDNLQVRGSD YSHSEDLADF PPSPDRDRES IV*

Position of stopcodon in wt / mu CDS

5889 / 5889

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

1963 / 1963

Position of stopcodon in wt / mu cDNA

5931 / 5931

Position of start ATG in wt / mu cDNA

43 / 43

Last intron/exon boundary

4693

Theoretical NMD boundary in CDS

4600

Length of CDS

5889

Coding sequence (CDS) position

5689

cDNA position

5731

gDNA position

99223

Chromosomal position

38550521

Speed

0.11 s

Back to summary table

Variant:

3:38550521C>A_6_ENST00000333535

Back to summary table

Prediction:

BenignPermalink

Summary:

Amino acid sequence changed
Homozygous in gnomAD
Protein features (might be) affected

Model: simple_aae
Tree vote: 28|72 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr3:38550521C>A (GRCh38)

Gene symbol

SCN5A

Gene constraints

LOEUF: 0.37, LOF (oe): 0.29, misssense (oe): 0.74, synonymous (oe): 0.91 ? (gnomAD)

Ensembl transcript ID

ENST00000333535.9

Genbank transcript ID

NM_198056 (by similarity)

UniProt / AlphaMissense peptide

SCN5A_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.5851G>T
g.99223G>T

AA changes

AAE:	V1951L	?
Score:	32

Frameshift

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs41315493
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	53	3115	3168

Protein conservation

Species	Match	AA	Alignment
Human		1951	D	A	P	E	R	E	G	L	I	A	Y	V	M	S	E	N	F	S	R	P	L	G	P	P
mutated	all conserved	1951	D	A	P	E	R	E	G	L	I	A	Y	L	M	S	E	N	F	S	R	P	L	G	P
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	2016	CHAIN		lost
1772	2016	TOPO_DOM	Cytoplasmic	lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.828	0.94
	0.927	0.931
(flanking)	1.413	0.912

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

Strand

-1

Original gDNA sequence snippet

GAGAGGGCCTCATCGCCTACGTGATGAGTGAGAACTTCTCC

Altered gDNA sequence snippet

GAGAGGGCCTCATCGCCTACTTGATGAGTGAGAACTTCTCC

Original cDNA sequence snippet

GAGAGGGCCTCATCGCCTACGTGATGAGTGAGAACTTCTCC

Altered cDNA sequence snippet

GAGAGGGCCTCATCGCCTACTTGATGAGTGAGAACTTCTCC

Wildtype AA sequence

MANFLLPRGT SSFRRFTRES LAAIEKRMAE KQARGSTTLQ ESREGLPEEE APRPQLDLQA
SKKLPDLYGN PPQELIGEPL EDLDPFYSTQ KTFIVLNKGK TIFRFSATNA LYVLSPFHPI
RRAAVKILVH SLFNMLIMCT ILTNCVFMAQ HDPPPWTKYV EYTFTAIYTF ESLVKILARG
FCLHAFTFLR DPWNWLDFSV IIMAYTTEFV DLGNVSALRT FRVLRALKTI SVISGLKTIV
GALIQSVKKL ADVMVLTVFC LSVFALIGLQ LFMGNLRHKC VRNFTALNGT NGSVEADGLV
WESLDLYLSD PENYLLKNGT SDVLLCGNSS DAGTCPEGYR CLKAGENPDH GYTSFDSFAW
AFLALFRLMT QDCWERLYQQ TLRSAGKIYM IFFMLVIFLG SFYLVNLILA VVAMAYEEQN
QATIAETEEK EKRFQEAMEM LKKEHEALTI RGVDTVSRSS LEMSPLAPVN SHERRSKRRK
RMSSGTEECG EDRLPKSDSE DGPRAMNHLS LTRGLSRTSM KPRSSRGSIF TFRRRDLGSE
ADFADDENST AGESESHHTS LLVPWPLRRT SAQGQPSPGT SAPGHALHGK KNSTVDCNGV
VSLLGAGDPE ATSPGSHLLR PVMLEHPPDT TTPSEEPGGP QMLTSQAPCV DGFEEPGARQ
RALSAVSVLT SALEELEESR HKCPPCWNRL AQRYLIWECC PLWMSIKQGV KLVVMDPFTD
LTITMCIVLN TLFMALEHYN MTSEFEEMLQ VGNLVFTGIF TAEMTFKIIA LDPYYYFQQG
WNIFDSIIVI LSLMELGLSR MSNLSVLRSF RLLRVFKLAK SWPTLNTLIK IIGNSVGALG
NLTLVLAIIV FIFAVVGMQL FGKNYSELRD SDSGLLPRWH MMDFFHAFLI IFRILCGEWI
ETMWDCMEVS GQSLCLLVFL LVMVIGNLVV LNLFLALLLS SFSADNLTAP DEDREMNNLQ
LALARIQRGL RFVKRTTWDF CCGLLRQRPQ KPAALAAQGQ LPSCIATPYS PPPPETEKVP
PTRKETRFEE GEQPGQGTPG DPEPVCVPIA VAESDTDDQE EDEENSLGTE EESSKQQESQ
PVSGGPEAPP DSRTWSQVSA TASSEAEASA SQADWRQQWK AEPQAPGCGE TPEDSCSEGS
TADMTNTAEL LEQIPDLGQD VKDPEDCFTE GCVRRCPCCA VDTTQAPGKV WWRLRKTCYH
IVEHSWFETF IIFMILLSSG ALAFEDIYLE ERKTIKVLLE YADKMFTYVF VLEMLLKWVA
YGFKKYFTNA WCWLDFLIVD VSLVSLVANT LGFAEMGPIK SLRTLRALRP LRALSRFEGM
RVVVNALVGA IPSIMNVLLV CLIFWLIFSI MGVNLFAGKF GRCINQTEGD LPLNYTIVNN
KSQCESLNLT GELYWTKVKV NFDNVGAGYL ALLQVATFKG WMDIMYAAVD SRGYEEQPQW
EYNLYMYIYF VIFIIFGSFF TLNLFIGVII DNFNQQKKKL GGQDIFMTEE QKKYYNAMKK
LGSKKPQKPI PRPLNKYQGF IFDIVTKQAF DVTIMFLICL NMVTMMVETD DQSPEKINIL
AKINLLFVAI FTGECIVKLA ALRHYYFTNS WNIFDFVVVI LSIVGTVLSD IIQKYFFSPT
LFRVIRLARI GRILRLIRGA KGIRTLLFAL MMSLPALFNI GLLLFLVMFI YSIFGMANFA
YVKWEAGIDD MFNFQTFANS MLCLFQITTS AGWDGLLSPI LNTGPPYCDP TLPNSNGSRG
DCGSPAVGIL FFTTYIIISF LIVVNMYIAI ILENFSVATE ESTEPLSEDD FDMFYEIWEK
FDPEATQFIE YSVLSDFADA LSEPLRIAKP NQISLINMDL PMVSGDRIHC MDILFAFTKR
VLGESGEMDA LKIQMEEKFM AANPSKISYE PITTTLRRKH EEVSAMVIQR AFRRHLLQRS
LKHASFLFRQ QAGSGLSEED APEREGLIAY VMSENFSRPL GPPSSSSISS TSFPPSYDSV
TRATSDNLQV RGSDYSHSED LADFPPSPDR DRESIV*

Mutated AA sequence

MANFLLPRGT SSFRRFTRES LAAIEKRMAE KQARGSTTLQ ESREGLPEEE APRPQLDLQA
SKKLPDLYGN PPQELIGEPL EDLDPFYSTQ KTFIVLNKGK TIFRFSATNA LYVLSPFHPI
RRAAVKILVH SLFNMLIMCT ILTNCVFMAQ HDPPPWTKYV EYTFTAIYTF ESLVKILARG
FCLHAFTFLR DPWNWLDFSV IIMAYTTEFV DLGNVSALRT FRVLRALKTI SVISGLKTIV
GALIQSVKKL ADVMVLTVFC LSVFALIGLQ LFMGNLRHKC VRNFTALNGT NGSVEADGLV
WESLDLYLSD PENYLLKNGT SDVLLCGNSS DAGTCPEGYR CLKAGENPDH GYTSFDSFAW
AFLALFRLMT QDCWERLYQQ TLRSAGKIYM IFFMLVIFLG SFYLVNLILA VVAMAYEEQN
QATIAETEEK EKRFQEAMEM LKKEHEALTI RGVDTVSRSS LEMSPLAPVN SHERRSKRRK
RMSSGTEECG EDRLPKSDSE DGPRAMNHLS LTRGLSRTSM KPRSSRGSIF TFRRRDLGSE
ADFADDENST AGESESHHTS LLVPWPLRRT SAQGQPSPGT SAPGHALHGK KNSTVDCNGV
VSLLGAGDPE ATSPGSHLLR PVMLEHPPDT TTPSEEPGGP QMLTSQAPCV DGFEEPGARQ
RALSAVSVLT SALEELEESR HKCPPCWNRL AQRYLIWECC PLWMSIKQGV KLVVMDPFTD
LTITMCIVLN TLFMALEHYN MTSEFEEMLQ VGNLVFTGIF TAEMTFKIIA LDPYYYFQQG
WNIFDSIIVI LSLMELGLSR MSNLSVLRSF RLLRVFKLAK SWPTLNTLIK IIGNSVGALG
NLTLVLAIIV FIFAVVGMQL FGKNYSELRD SDSGLLPRWH MMDFFHAFLI IFRILCGEWI
ETMWDCMEVS GQSLCLLVFL LVMVIGNLVV LNLFLALLLS SFSADNLTAP DEDREMNNLQ
LALARIQRGL RFVKRTTWDF CCGLLRQRPQ KPAALAAQGQ LPSCIATPYS PPPPETEKVP
PTRKETRFEE GEQPGQGTPG DPEPVCVPIA VAESDTDDQE EDEENSLGTE EESSKQQESQ
PVSGGPEAPP DSRTWSQVSA TASSEAEASA SQADWRQQWK AEPQAPGCGE TPEDSCSEGS
TADMTNTAEL LEQIPDLGQD VKDPEDCFTE GCVRRCPCCA VDTTQAPGKV WWRLRKTCYH
IVEHSWFETF IIFMILLSSG ALAFEDIYLE ERKTIKVLLE YADKMFTYVF VLEMLLKWVA
YGFKKYFTNA WCWLDFLIVD VSLVSLVANT LGFAEMGPIK SLRTLRALRP LRALSRFEGM
RVVVNALVGA IPSIMNVLLV CLIFWLIFSI MGVNLFAGKF GRCINQTEGD LPLNYTIVNN
KSQCESLNLT GELYWTKVKV NFDNVGAGYL ALLQVATFKG WMDIMYAAVD SRGYEEQPQW
EYNLYMYIYF VIFIIFGSFF TLNLFIGVII DNFNQQKKKL GGQDIFMTEE QKKYYNAMKK
LGSKKPQKPI PRPLNKYQGF IFDIVTKQAF DVTIMFLICL NMVTMMVETD DQSPEKINIL
AKINLLFVAI FTGECIVKLA ALRHYYFTNS WNIFDFVVVI LSIVGTVLSD IIQKYFFSPT
LFRVIRLARI GRILRLIRGA KGIRTLLFAL MMSLPALFNI GLLLFLVMFI YSIFGMANFA
YVKWEAGIDD MFNFQTFANS MLCLFQITTS AGWDGLLSPI LNTGPPYCDP TLPNSNGSRG
DCGSPAVGIL FFTTYIIISF LIVVNMYIAI ILENFSVATE ESTEPLSEDD FDMFYEIWEK
FDPEATQFIE YSVLSDFADA LSEPLRIAKP NQISLINMDL PMVSGDRIHC MDILFAFTKR
VLGESGEMDA LKIQMEEKFM AANPSKISYE PITTTLRRKH EEVSAMVIQR AFRRHLLQRS
LKHASFLFRQ QAGSGLSEED APEREGLIAY LMSENFSRPL GPPSSSSISS TSFPPSYDSV
TRATSDNLQV RGSDYSHSED LADFPPSPDR DRESIV*

Position of stopcodon in wt / mu CDS

6051 / 6051

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

2017 / 2017

Position of stopcodon in wt / mu cDNA

6260 / 6260

Position of start ATG in wt / mu cDNA

210 / 210

Last intron/exon boundary

5022

Theoretical NMD boundary in CDS

4762

Length of CDS

6051

Coding sequence (CDS) position

5851

cDNA position

6060

gDNA position

99223

Chromosomal position

38550521

Speed

0.13 s

Back to summary table

Variant:

3:38550521C>A_7_ENST00000327956

Back to summary table

Prediction:

BenignPermalink

Summary:

Amino acid sequence changed
Homozygous in gnomAD
Protein features (might be) affected

Model: simple_aae
Tree vote: 28|72 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr3:38550521C>A (GRCh38)

Gene symbol

SCN5A

Gene constraints

LOEUF: 0.99, LOF (oe): 0.21, misssense (oe): 0.93, synonymous (oe): 0.90 ? (gnomAD)

Ensembl transcript ID

ENST00000327956.7

Genbank transcript ID

UniProt / AlphaMissense peptide

SCN5A_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.5848G>T
g.99223G>T

AA changes

AAE:	V1950L	?
Score:	32

Frameshift

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs41315493
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	53	3115	3168

Protein conservation

Species	Match	AA	Alignment
Human		1950	D	A	P	E	R	E	G	L	I	A	Y	V	M	S	E	N	F	S	R	P	L	G	P	P
mutated	all conserved	1950	D	A	P	E	R	E	G	L	I	A	Y	L	M	S	E	N	F	S	R	P	L	G	P
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	2016	CHAIN		lost
1772	2016	TOPO_DOM	Cytoplasmic	lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.828	0.94
	0.927	0.931
(flanking)	1.413	0.912

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

Strand

-1

Original gDNA sequence snippet

GAGAGGGCCTCATCGCCTACGTGATGAGTGAGAACTTCTCC

Altered gDNA sequence snippet

GAGAGGGCCTCATCGCCTACTTGATGAGTGAGAACTTCTCC

Original cDNA sequence snippet

GAGAGGGCCTCATCGCCTACGTGATGAGTGAGAACTTCTCC

Altered cDNA sequence snippet

GAGAGGGCCTCATCGCCTACTTGATGAGTGAGAACTTCTCC

Wildtype AA sequence

MANFLLPRGT SSFRRFTRES LAAIEKRMAE KQARGSTTLQ ESREGLPEEE APRPQLDLQA
SKKLPDLYGN PPQELIGEPL EDLDPFYSTQ KTFIVLNKGK TIFRFSATNA LYVLSPFHPI
RRAAVKILVH SLFNMLIMCT ILTNCVFMAQ HDPPPWTKYV EYTFTAIYTF ESLVKILARG
FCLHAFTFLR DPWNWLDFSV IIMAYTTEFV DLGNVSALRT FRVLRALKTI SVISGLKTIV
GALIQSVKKL ADVMVLTVFC LSVFALIGLQ LFMGNLRHKC VRNFTALNGT NGSVEADGLV
WESLDLYLSD PENYLLKNGT SDVLLCGNSS DAGTCPEGYR CLKAGENPDH GYTSFDSFAW
AFLALFRLMT QDCWERLYQQ TLRSAGKIYM IFFMLVIFLG SFYLVNLILA VVAMAYEEQN
QATIAETEEK EKRFQEAMEM LKKEHEALTI RGVDTVSRSS LEMSPLAPVN SHERRSKRRK
RMSSGTEECG EDRLPKSDSE DGPRAMNHLS LTRGLSRTSM KPRSSRGSIF TFRRRDLGSE
ADFADDENST AGESESHHTS LLVPWPLRRT SAQGQPSPGT SAPGHALHGK KNSTVDCNGV
VSLLGAGDPE ATSPGSHLLR PVMLEHPPDT TTPSEEPGGP QMLTSQAPCV DGFEEPGARQ
RALSAVSVLT SALEELEESR HKCPPCWNRL AQRYLIWECC PLWMSIKQGV KLVVMDPFTD
LTITMCIVLN TLFMALEHYN MTSEFEEMLQ VGNLVFTGIF TAEMTFKIIA LDPYYYFQQG
WNIFDSIIVI LSLMELGLSR MSNLSVLRSF RLLRVFKLAK SWPTLNTLIK IIGNSVGALG
NLTLVLAIIV FIFAVVGMQL FGKNYSELRD SDSGLLPRWH MMDFFHAFLI IFRILCGEWI
ETMWDCMEVS GQSLCLLVFL LVMVIGNLVV LNLFLALLLS SFSADNLTAP DEDREMNNLQ
LALARIQRGL RFVKRTTWDF CCGLLRQRPQ KPAALAAQGQ LPSCIATPYS PPPPETEKVP
PTRKETRFEE GEQPGQGTPG DPEPVCVPIA VAESDTDDQE EDEENSLGTE EESSKQESQP
VSGGPEAPPD SRTWSQVSAT ASSEAEASAS QADWRQQWKA EPQAPGCGET PEDSCSEGST
ADMTNTAELL EQIPDLGQDV KDPEDCFTEG CVRRCPCCAV DTTQAPGKVW WRLRKTCYHI
VEHSWFETFI IFMILLSSGA LAFEDIYLEE RKTIKVLLEY ADKMFTYVFV LEMLLKWVAY
GFKKYFTNAW CWLDFLIVDV SLVSLVANTL GFAEMGPIKS LRTLRALRPL RALSRFEGMR
VVVNALVGAI PSIMNVLLVC LIFWLIFSIM GVNLFAGKFG RCINQTEGDL PLNYTIVNNK
SQCESLNLTG ELYWTKVKVN FDNVGAGYLA LLQVATFKGW MDIMYAAVDS RGYEEQPQWE
YNLYMYIYFV IFIIFGSFFT LNLFIGVIID NFNQQKKKLG GQDIFMTEEQ KKYYNAMKKL
GSKKPQKPIP RPLNKYQGFI FDIVTKQAFD VTIMFLICLN MVTMMVETDD QSPEKINILA
KINLLFVAIF TGECIVKLAA LRHYYFTNSW NIFDFVVVIL SIVGTVLSDI IQKYFFSPTL
FRVIRLARIG RILRLIRGAK GIRTLLFALM MSLPALFNIG LLLFLVMFIY SIFGMANFAY
VKWEAGIDDM FNFQTFANSM LCLFQITTSA GWDGLLSPIL NTGPPYCDPT LPNSNGSRGD
CGSPAVGILF FTTYIIISFL IVVNMYIAII LENFSVATEE STEPLSEDDF DMFYEIWEKF
DPEATQFIEY SVLSDFADAL SEPLRIAKPN QISLINMDLP MVSGDRIHCM DILFAFTKRV
LGESGEMDAL KIQMEEKFMA ANPSKISYEP ITTTLRRKHE EVSAMVIQRA FRRHLLQRSL
KHASFLFRQQ AGSGLSEEDA PEREGLIAYV MSENFSRPLG PPSSSSISST SFPPSYDSVT
RATSDNLQVR GSDYSHSEDL ADFPPSPDRD RESIV*

Mutated AA sequence

MANFLLPRGT SSFRRFTRES LAAIEKRMAE KQARGSTTLQ ESREGLPEEE APRPQLDLQA
SKKLPDLYGN PPQELIGEPL EDLDPFYSTQ KTFIVLNKGK TIFRFSATNA LYVLSPFHPI
RRAAVKILVH SLFNMLIMCT ILTNCVFMAQ HDPPPWTKYV EYTFTAIYTF ESLVKILARG
FCLHAFTFLR DPWNWLDFSV IIMAYTTEFV DLGNVSALRT FRVLRALKTI SVISGLKTIV
GALIQSVKKL ADVMVLTVFC LSVFALIGLQ LFMGNLRHKC VRNFTALNGT NGSVEADGLV
WESLDLYLSD PENYLLKNGT SDVLLCGNSS DAGTCPEGYR CLKAGENPDH GYTSFDSFAW
AFLALFRLMT QDCWERLYQQ TLRSAGKIYM IFFMLVIFLG SFYLVNLILA VVAMAYEEQN
QATIAETEEK EKRFQEAMEM LKKEHEALTI RGVDTVSRSS LEMSPLAPVN SHERRSKRRK
RMSSGTEECG EDRLPKSDSE DGPRAMNHLS LTRGLSRTSM KPRSSRGSIF TFRRRDLGSE
ADFADDENST AGESESHHTS LLVPWPLRRT SAQGQPSPGT SAPGHALHGK KNSTVDCNGV
VSLLGAGDPE ATSPGSHLLR PVMLEHPPDT TTPSEEPGGP QMLTSQAPCV DGFEEPGARQ
RALSAVSVLT SALEELEESR HKCPPCWNRL AQRYLIWECC PLWMSIKQGV KLVVMDPFTD
LTITMCIVLN TLFMALEHYN MTSEFEEMLQ VGNLVFTGIF TAEMTFKIIA LDPYYYFQQG
WNIFDSIIVI LSLMELGLSR MSNLSVLRSF RLLRVFKLAK SWPTLNTLIK IIGNSVGALG
NLTLVLAIIV FIFAVVGMQL FGKNYSELRD SDSGLLPRWH MMDFFHAFLI IFRILCGEWI
ETMWDCMEVS GQSLCLLVFL LVMVIGNLVV LNLFLALLLS SFSADNLTAP DEDREMNNLQ
LALARIQRGL RFVKRTTWDF CCGLLRQRPQ KPAALAAQGQ LPSCIATPYS PPPPETEKVP
PTRKETRFEE GEQPGQGTPG DPEPVCVPIA VAESDTDDQE EDEENSLGTE EESSKQESQP
VSGGPEAPPD SRTWSQVSAT ASSEAEASAS QADWRQQWKA EPQAPGCGET PEDSCSEGST
ADMTNTAELL EQIPDLGQDV KDPEDCFTEG CVRRCPCCAV DTTQAPGKVW WRLRKTCYHI
VEHSWFETFI IFMILLSSGA LAFEDIYLEE RKTIKVLLEY ADKMFTYVFV LEMLLKWVAY
GFKKYFTNAW CWLDFLIVDV SLVSLVANTL GFAEMGPIKS LRTLRALRPL RALSRFEGMR
VVVNALVGAI PSIMNVLLVC LIFWLIFSIM GVNLFAGKFG RCINQTEGDL PLNYTIVNNK
SQCESLNLTG ELYWTKVKVN FDNVGAGYLA LLQVATFKGW MDIMYAAVDS RGYEEQPQWE
YNLYMYIYFV IFIIFGSFFT LNLFIGVIID NFNQQKKKLG GQDIFMTEEQ KKYYNAMKKL
GSKKPQKPIP RPLNKYQGFI FDIVTKQAFD VTIMFLICLN MVTMMVETDD QSPEKINILA
KINLLFVAIF TGECIVKLAA LRHYYFTNSW NIFDFVVVIL SIVGTVLSDI IQKYFFSPTL
FRVIRLARIG RILRLIRGAK GIRTLLFALM MSLPALFNIG LLLFLVMFIY SIFGMANFAY
VKWEAGIDDM FNFQTFANSM LCLFQITTSA GWDGLLSPIL NTGPPYCDPT LPNSNGSRGD
CGSPAVGILF FTTYIIISFL IVVNMYIAII LENFSVATEE STEPLSEDDF DMFYEIWEKF
DPEATQFIEY SVLSDFADAL SEPLRIAKPN QISLINMDLP MVSGDRIHCM DILFAFTKRV
LGESGEMDAL KIQMEEKFMA ANPSKISYEP ITTTLRRKHE EVSAMVIQRA FRRHLLQRSL
KHASFLFRQQ AGSGLSEEDA PEREGLIAYL MSENFSRPLG PPSSSSISST SFPPSYDSVT
RATSDNLQVR GSDYSHSEDL ADFPPSPDRD RESIV*

Position of stopcodon in wt / mu CDS

6048 / 6048

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

2016 / 2016

Position of stopcodon in wt / mu cDNA

6186 / 6186

Position of start ATG in wt / mu cDNA

139 / 139

Last intron/exon boundary

4948

Theoretical NMD boundary in CDS

4759

Length of CDS

6048

Coding sequence (CDS) position

5848

cDNA position

5986

gDNA position

99223

Chromosomal position

38550521

Speed

0.05 s

Back to summary table

Variant:

3:38550521C>A_8_ENST00000414099

Back to summary table

Prediction:

BenignPermalink

Summary:

Amino acid sequence changed
Homozygous in gnomAD

Model: simple_aae
Tree vote: 28|72 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr3:38550521C>A (GRCh38)

Gene symbol

SCN5A

Gene constraints

LOEUF: 0.36, LOF (oe): 0.28, misssense (oe): 0.75, synonymous (oe): 0.91 ? (gnomAD)

Ensembl transcript ID

ENST00000414099.6

Genbank transcript ID

NM_001354701 (by similarity), NM_001099405 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.5797G>T
g.99223G>T

AA changes

AAE:	V1933L	?
Score:	32

Frameshift

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs41315493
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	53	3115	3168

Protein conservation

Species	Match	AA	Alignment
Human		1933	D	A	P	E	R	E	G	L	I	A	Y	V	M	S	E	N	F	S	R	P	L	G	P	P
mutated	all conserved	1933	D	A	P	E	R	E	G	L	I	A	Y	L	M	S	E	N	F	S	R	P	L	G	P
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)	0.828	0.94
	0.927	0.931
(flanking)	1.413	0.912

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

Strand

-1

Original gDNA sequence snippet

GAGAGGGCCTCATCGCCTACGTGATGAGTGAGAACTTCTCC

Altered gDNA sequence snippet

GAGAGGGCCTCATCGCCTACTTGATGAGTGAGAACTTCTCC

Original cDNA sequence snippet

GAGAGGGCCTCATCGCCTACGTGATGAGTGAGAACTTCTCC

Altered cDNA sequence snippet

GAGAGGGCCTCATCGCCTACTTGATGAGTGAGAACTTCTCC

Wildtype AA sequence

MANFLLPRGT SSFRRFTRES LAAIEKRMAE KQARGSTTLQ ESREGLPEEE APRPQLDLQA
SKKLPDLYGN PPQELIGEPL EDLDPFYSTQ KTFIVLNKGK TIFRFSATNA LYVLSPFHPI
RRAAVKILVH SLFNMLIMCT ILTNCVFMAQ HDPPPWTKYV EYTFTAIYTF ESLVKILARG
FCLHAFTFLR DPWNWLDFSV IIMAYVSENI KLGNLSALRT FRVLRALKTI SVIPGLKTIV
GALIQSVKKL ADVMVLTVFC LSVFALIGLQ LFMGNLRHKC VRNFTALNGT NGSVEADGLV
WESLDLYLSD PENYLLKNGT SDVLLCGNSS DAGTCPEGYR CLKAGENPDH GYTSFDSFAW
AFLALFRLMT QDCWERLYQQ TLRSAGKIYM IFFMLVIFLG SFYLVNLILA VVAMAYEEQN
QATIAETEEK EKRFQEAMEM LKKEHEALTI RGVDTVSRSS LEMSPLAPVN SHERRSKRRK
RMSSGTEECG EDRLPKSDSE DGPRAMNHLS LTRGLSRTSM KPRSSRGSIF TFRRRDLGSE
ADFADDENST AGESESHHTS LLVPWPLRRT SAQGQPSPGT SAPGHALHGK KNSTVDCNGV
VSLLGAGDPE ATSPGSHLLR PVMLEHPPDT TTPSEEPGGP QMLTSQAPCV DGFEEPGARQ
RALSAVSVLT SALEELEESR HKCPPCWNRL AQRYLIWECC PLWMSIKQGV KLVVMDPFTD
LTITMCIVLN TLFMALEHYN MTSEFEEMLQ VGNLVFTGIF TAEMTFKIIA LDPYYYFQQG
WNIFDSIIVI LSLMELGLSR MSNLSVLRSF RLLRVFKLAK SWPTLNTLIK IIGNSVGALG
NLTLVLAIIV FIFAVVGMQL FGKNYSELRD SDSGLLPRWH MMDFFHAFLI IFRILCGEWI
ETMWDCMEVS GQSLCLLVFL LVMVIGNLVV LNLFLALLLS SFSADNLTAP DEDREMNNLQ
LALARIQRGL RFVKRTTWDF CCGLLRQRPQ KPAALAAQGQ LPSCIATPYS PPPPETEKVP
PTRKETRFEE GEQPGQGTPG DPEPVCVPIA VAESDTDDQE EDEENSLGTE EESSKQQESQ
PVSGGPEAPP DSRTWSQVSA TASSEAEASA SQADWRQQWK AEPQAPGCGE TPEDSCSEGS
TADMTNTAEL LEQIPDLGQD VKDPEDCFTE GCVRRCPCCA VDTTQAPGKV WWRLRKTCYH
IVEHSWFETF IIFMILLSSG ALAFEDIYLE ERKTIKVLLE YADKMFTYVF VLEMLLKWVA
YGFKKYFTNA WCWLDFLIVD VSLVSLVANT LGFAEMGPIK SLRTLRALRP LRALSRFEGM
RVVVNALVGA IPSIMNVLLV CLIFWLIFSI MGVNLFAGKF GRCINQTEGD LPLNYTIVNN
KSQCESLNLT GELYWTKVKV NFDNVGAGYL ALLQVYEEQP QWEYNLYMYI YFVIFIIFGS
FFTLNLFIGV IIDNFNQQKK KLGGQDIFMT EEQKKYYNAM KKLGSKKPQK PIPRPLNKYQ
GFIFDIVTKQ AFDVTIMFLI CLNMVTMMVE TDDQSPEKIN ILAKINLLFV AIFTGECIVK
LAALRHYYFT NSWNIFDFVV VILSIVGTVL SDIIQKYFFS PTLFRVIRLA RIGRILRLIR
GAKGIRTLLF ALMMSLPALF NIGLLLFLVM FIYSIFGMAN FAYVKWEAGI DDMFNFQTFA
NSMLCLFQIT TSAGWDGLLS PILNTGPPYC DPTLPNSNGS RGDCGSPAVG ILFFTTYIII
SFLIVVNMYI AIILENFSVA TEESTEPLSE DDFDMFYEIW EKFDPEATQF IEYSVLSDFA
DALSEPLRIA KPNQISLINM DLPMVSGDRI HCMDILFAFT KRVLGESGEM DALKIQMEEK
FMAANPSKIS YEPITTTLRR KHEEVSAMVI QRAFRRHLLQ RSLKHASFLF RQQAGSGLSE
EDAPEREGLI AYVMSENFSR PLGPPSSSSI SSTSFPPSYD SVTRATSDNL QVRGSDYSHS
EDLADFPPSP DRDRESIV*

Mutated AA sequence

MANFLLPRGT SSFRRFTRES LAAIEKRMAE KQARGSTTLQ ESREGLPEEE APRPQLDLQA
SKKLPDLYGN PPQELIGEPL EDLDPFYSTQ KTFIVLNKGK TIFRFSATNA LYVLSPFHPI
RRAAVKILVH SLFNMLIMCT ILTNCVFMAQ HDPPPWTKYV EYTFTAIYTF ESLVKILARG
FCLHAFTFLR DPWNWLDFSV IIMAYVSENI KLGNLSALRT FRVLRALKTI SVIPGLKTIV
GALIQSVKKL ADVMVLTVFC LSVFALIGLQ LFMGNLRHKC VRNFTALNGT NGSVEADGLV
WESLDLYLSD PENYLLKNGT SDVLLCGNSS DAGTCPEGYR CLKAGENPDH GYTSFDSFAW
AFLALFRLMT QDCWERLYQQ TLRSAGKIYM IFFMLVIFLG SFYLVNLILA VVAMAYEEQN
QATIAETEEK EKRFQEAMEM LKKEHEALTI RGVDTVSRSS LEMSPLAPVN SHERRSKRRK
RMSSGTEECG EDRLPKSDSE DGPRAMNHLS LTRGLSRTSM KPRSSRGSIF TFRRRDLGSE
ADFADDENST AGESESHHTS LLVPWPLRRT SAQGQPSPGT SAPGHALHGK KNSTVDCNGV
VSLLGAGDPE ATSPGSHLLR PVMLEHPPDT TTPSEEPGGP QMLTSQAPCV DGFEEPGARQ
RALSAVSVLT SALEELEESR HKCPPCWNRL AQRYLIWECC PLWMSIKQGV KLVVMDPFTD
LTITMCIVLN TLFMALEHYN MTSEFEEMLQ VGNLVFTGIF TAEMTFKIIA LDPYYYFQQG
WNIFDSIIVI LSLMELGLSR MSNLSVLRSF RLLRVFKLAK SWPTLNTLIK IIGNSVGALG
NLTLVLAIIV FIFAVVGMQL FGKNYSELRD SDSGLLPRWH MMDFFHAFLI IFRILCGEWI
ETMWDCMEVS GQSLCLLVFL LVMVIGNLVV LNLFLALLLS SFSADNLTAP DEDREMNNLQ
LALARIQRGL RFVKRTTWDF CCGLLRQRPQ KPAALAAQGQ LPSCIATPYS PPPPETEKVP
PTRKETRFEE GEQPGQGTPG DPEPVCVPIA VAESDTDDQE EDEENSLGTE EESSKQQESQ
PVSGGPEAPP DSRTWSQVSA TASSEAEASA SQADWRQQWK AEPQAPGCGE TPEDSCSEGS
TADMTNTAEL LEQIPDLGQD VKDPEDCFTE GCVRRCPCCA VDTTQAPGKV WWRLRKTCYH
IVEHSWFETF IIFMILLSSG ALAFEDIYLE ERKTIKVLLE YADKMFTYVF VLEMLLKWVA
YGFKKYFTNA WCWLDFLIVD VSLVSLVANT LGFAEMGPIK SLRTLRALRP LRALSRFEGM
RVVVNALVGA IPSIMNVLLV CLIFWLIFSI MGVNLFAGKF GRCINQTEGD LPLNYTIVNN
KSQCESLNLT GELYWTKVKV NFDNVGAGYL ALLQVYEEQP QWEYNLYMYI YFVIFIIFGS
FFTLNLFIGV IIDNFNQQKK KLGGQDIFMT EEQKKYYNAM KKLGSKKPQK PIPRPLNKYQ
GFIFDIVTKQ AFDVTIMFLI CLNMVTMMVE TDDQSPEKIN ILAKINLLFV AIFTGECIVK
LAALRHYYFT NSWNIFDFVV VILSIVGTVL SDIIQKYFFS PTLFRVIRLA RIGRILRLIR
GAKGIRTLLF ALMMSLPALF NIGLLLFLVM FIYSIFGMAN FAYVKWEAGI DDMFNFQTFA
NSMLCLFQIT TSAGWDGLLS PILNTGPPYC DPTLPNSNGS RGDCGSPAVG ILFFTTYIII
SFLIVVNMYI AIILENFSVA TEESTEPLSE DDFDMFYEIW EKFDPEATQF IEYSVLSDFA
DALSEPLRIA KPNQISLINM DLPMVSGDRI HCMDILFAFT KRVLGESGEM DALKIQMEEK
FMAANPSKIS YEPITTTLRR KHEEVSAMVI QRAFRRHLLQ RSLKHASFLF RQQAGSGLSE
EDAPEREGLI AYLMSENFSR PLGPPSSSSI SSTSFPPSYD SVTRATSDNL QVRGSDYSHS
EDLADFPPSP DRDRESIV*

Position of stopcodon in wt / mu CDS

5997 / 5997

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

1999 / 1999

Position of stopcodon in wt / mu cDNA

6039 / 6039

Position of start ATG in wt / mu cDNA

43 / 43

Last intron/exon boundary

4801

Theoretical NMD boundary in CDS

4708

Length of CDS

5997

Coding sequence (CDS) position

5797

cDNA position

5839

gDNA position

99223

Chromosomal position

38550521

Speed

0.05 s

Back to summary table

Variant:

3:38550521C>A_5_ENST00000449557

Back to summary table

Prediction:

BenignPermalink

Summary:

Amino acid sequence changed
Homozygous in gnomAD

Model: simple_aae
Tree vote: 29|71 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr3:38550521C>A (GRCh38)

Gene symbol

SCN5A

Gene constraints

LOEUF: 0.36, LOF (oe): 0.28, misssense (oe): 0.73, synonymous (oe): 0.91 ? (gnomAD)

Ensembl transcript ID

ENST00000449557.6

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.5689G>T
g.99223G>T

AA changes

AAE:	V1897L	?
Score:	32

Frameshift

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs41315493
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	53	3115	3168

Protein conservation

Species	Match	AA	Alignment
Human		1897	D	A	P	E	R	E	G	L	I	A	Y	V	M	S	E	N	F	S	R	P	L	G	P	P
mutated	all conserved	1897	D	A	P	E	R	E	G	L	I	A	Y	L	M	S	E	N	F	S	R	P	L	G	P
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)	0.828	0.94
	0.927	0.931
(flanking)	1.413	0.912

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

Strand

-1

Original gDNA sequence snippet

GAGAGGGCCTCATCGCCTACGTGATGAGTGAGAACTTCTCC

Altered gDNA sequence snippet

GAGAGGGCCTCATCGCCTACTTGATGAGTGAGAACTTCTCC

Original cDNA sequence snippet

GAGAGGGCCTCATCGCCTACGTGATGAGTGAGAACTTCTCC

Altered cDNA sequence snippet

GAGAGGGCCTCATCGCCTACTTGATGAGTGAGAACTTCTCC

Wildtype AA sequence

MANFLLPRGT SSFRRFTRES LAAIEKRMAE KQARGSTTLQ ESREGLPEEE APRPQLDLQA
SKKLPDLYGN PPQELIGEPL EDLDPFYSTQ KTFIVLNKGK TIFRFSATNA LYVLSPFHPI
RRAAVKILVH SLFNMLIMCT ILTNCVFMAQ HDPPPWTKYV EYTFTAIYTF ESLVKILARG
FCLHAFTFLR DPWNWLDFSV IIMAYTTEFV DLGNVSALRT FRVLRALKTI SVISGLKTIV
GALIQSVKKL ADVMVLTVFC LSVFALIGLQ LFMGNLRHKC VRNFTALNGT NGSVEADGLV
WESLDLYLSD PENYLLKNGT SDVLLCGNSS DAGTCPEGYR CLKAGENPDH GYTSFDSFAW
AFLALFRLMT QDCWERLYQQ TLRSAGKIYM IFFMLVIFLG SFYLVNLILA VVAMAYEEQN
QATIAETEEK EKRFQEAMEM LKKEHEALTI RGVDTVSRSS LEMSPLAPVN SHERRSKRRK
RMSSGTEECG EDRLPKSDSE DGPRAMNHLS LTRGLSRTSM KPRSSRGSIF TFRRRDLGSE
ADFADDENST AGESESHHTS LLVPWPLRRT SAQGQPSPGT SAPGHALHGK KNSTVDCNGV
VSLLGAGDPE ATSPGSHLLR PVMLEHPPDT TTPSEEPGGP QMLTSQAPCV DGFEEPGARQ
RALSAVSVLT SALEELEESR HKCPPCWNRL AQRYLIWECC PLWMSIKQGV KLVVMDPFTD
LTITMCIVLN TLFMALEHYN MTSEFEEMLQ VGNLVFTGIF TAEMTFKIIA LDPYYYFQQG
WNIFDSIIVI LSLMELGLSR MSNLSVLRSF RLLRVFKLAK SWPTLNTLIK IIGNSVGALG
NLTLVLAIIV FIFAVVGMQL FGKNYSELRD SDSGLLPRWH MMDFFHAFLI IFRILCGEWI
ETMWDCMEVS GQSLCLLVFL LVMVIGNLVV LNLFLALLLS SFSADNLTAP DEDREMNNLQ
LALARIQRGL RFVKRTTWDF CCGLLRQRPQ KPAALAAQGQ LPSCIATPYS PPPPETEKVP
PTRKETRFEE GEQPGQGTPG DPEPVCVPIA VAESDTDDQE EDEENSLGTE EESSKQTPED
SCSEGSTADM TNTAELLEQI PDLGQDVKDP EDCFTEGCVR RCPCCAVDTT QAPGKVWWRL
RKTCYHIVEH SWFETFIIFM ILLSSGALAF EDIYLEERKT IKVLLEYADK MFTYVFVLEM
LLKWVAYGFK KYFTNAWCWL DFLIVDVSLV SLVANTLGFA EMGPIKSLRT LRALRPLRAL
SRFEGMRVVV NALVGAIPSI MNVLLVCLIF WLIFSIMGVN LFAGKFGRCI NQTEGDLPLN
YTIVNNKSQC ESLNLTGELY WTKVKVNFDN VGAGYLALLQ VATFKGWMDI MYAAVDSRGY
EEQPQWEYNL YMYIYFVIFI IFGSFFTLNL FIGVIIDNFN QQKKKLGGQD IFMTEEQKKY
YNAMKKLGSK KPQKPIPRPL NKYQGFIFDI VTKQAFDVTI MFLICLNMVT MMVETDDQSP
EKINILAKIN LLFVAIFTGE CIVKLAALRH YYFTNSWNIF DFVVVILSIV GTVLSDIIQK
YFFSPTLFRV IRLARIGRIL RLIRGAKGIR TLLFALMMSL PALFNIGLLL FLVMFIYSIF
GMANFAYVKW EAGIDDMFNF QTFANSMLCL FQITTSAGWD GLLSPILNTG PPYCDPTLPN
SNGSRGDCGS PAVGILFFTT YIIISFLIVV NMYIAIILEN FSVATEESTE PLSEDDFDMF
YEIWEKFDPE ATQFIEYSVL SDFADALSEP LRIAKPNQIS LINMDLPMVS GDRIHCMDIL
FAFTKRVLGE SGEMDALKIQ MEEKFMAANP SKISYEPITT TLRRKHEEVS AMVIQRAFRR
HLLQRSLKHA SFLFRQQAGS GLSEEDAPER EGLIAYVMSE NFSRPLGPPS SSSISSTSFP
PSYDSVTRAT SDNLQVRGSD YSHSEDLADF PPSPDRDRES IV*

Mutated AA sequence

MANFLLPRGT SSFRRFTRES LAAIEKRMAE KQARGSTTLQ ESREGLPEEE APRPQLDLQA
SKKLPDLYGN PPQELIGEPL EDLDPFYSTQ KTFIVLNKGK TIFRFSATNA LYVLSPFHPI
RRAAVKILVH SLFNMLIMCT ILTNCVFMAQ HDPPPWTKYV EYTFTAIYTF ESLVKILARG
FCLHAFTFLR DPWNWLDFSV IIMAYTTEFV DLGNVSALRT FRVLRALKTI SVISGLKTIV
GALIQSVKKL ADVMVLTVFC LSVFALIGLQ LFMGNLRHKC VRNFTALNGT NGSVEADGLV
WESLDLYLSD PENYLLKNGT SDVLLCGNSS DAGTCPEGYR CLKAGENPDH GYTSFDSFAW
AFLALFRLMT QDCWERLYQQ TLRSAGKIYM IFFMLVIFLG SFYLVNLILA VVAMAYEEQN
QATIAETEEK EKRFQEAMEM LKKEHEALTI RGVDTVSRSS LEMSPLAPVN SHERRSKRRK
RMSSGTEECG EDRLPKSDSE DGPRAMNHLS LTRGLSRTSM KPRSSRGSIF TFRRRDLGSE
ADFADDENST AGESESHHTS LLVPWPLRRT SAQGQPSPGT SAPGHALHGK KNSTVDCNGV
VSLLGAGDPE ATSPGSHLLR PVMLEHPPDT TTPSEEPGGP QMLTSQAPCV DGFEEPGARQ
RALSAVSVLT SALEELEESR HKCPPCWNRL AQRYLIWECC PLWMSIKQGV KLVVMDPFTD
LTITMCIVLN TLFMALEHYN MTSEFEEMLQ VGNLVFTGIF TAEMTFKIIA LDPYYYFQQG
WNIFDSIIVI LSLMELGLSR MSNLSVLRSF RLLRVFKLAK SWPTLNTLIK IIGNSVGALG
NLTLVLAIIV FIFAVVGMQL FGKNYSELRD SDSGLLPRWH MMDFFHAFLI IFRILCGEWI
ETMWDCMEVS GQSLCLLVFL LVMVIGNLVV LNLFLALLLS SFSADNLTAP DEDREMNNLQ
LALARIQRGL RFVKRTTWDF CCGLLRQRPQ KPAALAAQGQ LPSCIATPYS PPPPETEKVP
PTRKETRFEE GEQPGQGTPG DPEPVCVPIA VAESDTDDQE EDEENSLGTE EESSKQTPED
SCSEGSTADM TNTAELLEQI PDLGQDVKDP EDCFTEGCVR RCPCCAVDTT QAPGKVWWRL
RKTCYHIVEH SWFETFIIFM ILLSSGALAF EDIYLEERKT IKVLLEYADK MFTYVFVLEM
LLKWVAYGFK KYFTNAWCWL DFLIVDVSLV SLVANTLGFA EMGPIKSLRT LRALRPLRAL
SRFEGMRVVV NALVGAIPSI MNVLLVCLIF WLIFSIMGVN LFAGKFGRCI NQTEGDLPLN
YTIVNNKSQC ESLNLTGELY WTKVKVNFDN VGAGYLALLQ VATFKGWMDI MYAAVDSRGY
EEQPQWEYNL YMYIYFVIFI IFGSFFTLNL FIGVIIDNFN QQKKKLGGQD IFMTEEQKKY
YNAMKKLGSK KPQKPIPRPL NKYQGFIFDI VTKQAFDVTI MFLICLNMVT MMVETDDQSP
EKINILAKIN LLFVAIFTGE CIVKLAALRH YYFTNSWNIF DFVVVILSIV GTVLSDIIQK
YFFSPTLFRV IRLARIGRIL RLIRGAKGIR TLLFALMMSL PALFNIGLLL FLVMFIYSIF
GMANFAYVKW EAGIDDMFNF QTFANSMLCL FQITTSAGWD GLLSPILNTG PPYCDPTLPN
SNGSRGDCGS PAVGILFFTT YIIISFLIVV NMYIAIILEN FSVATEESTE PLSEDDFDMF
YEIWEKFDPE ATQFIEYSVL SDFADALSEP LRIAKPNQIS LINMDLPMVS GDRIHCMDIL
FAFTKRVLGE SGEMDALKIQ MEEKFMAANP SKISYEPITT TLRRKHEEVS AMVIQRAFRR
HLLQRSLKHA SFLFRQQAGS GLSEEDAPER EGLIAYLMSE NFSRPLGPPS SSSISSTSFP
PSYDSVTRAT SDNLQVRGSD YSHSEDLADF PPSPDRDRES IV*

Position of stopcodon in wt / mu CDS

5889 / 5889

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

1963 / 1963

Position of stopcodon in wt / mu cDNA

5898 / 5898

Position of start ATG in wt / mu cDNA

10 / 10

Last intron/exon boundary

4660

Theoretical NMD boundary in CDS

4600

Length of CDS

5889

Coding sequence (CDS) position

5689

cDNA position

5698

gDNA position

99223

Chromosomal position

38550521

Speed

0.05 s

Back to summary table

Variant:

3:38550521C>A_2_ENST00000423572

Back to summary table

Prediction:

BenignPermalink

Summary:

Amino acid sequence changed
Homozygous in gnomAD
Protein features (might be) affected

Model: simple_aae
Tree vote: 30|70 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr3:38550521C>A (GRCh38)

Gene symbol

SCN5A

Gene constraints

LOEUF: 0.37, LOF (oe): 0.29, misssense (oe): 0.74, synonymous (oe): 0.91 ? (gnomAD)

Ensembl transcript ID

ENST00000423572.7

Genbank transcript ID

NM_000335 (exact from MANE)

UniProt / AlphaMissense peptide

SCN5A_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.5848G>T
g.99223G>T

AA changes

AAE:	V1950L	?
Score:	32

Frameshift

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs41315493
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	53	3115	3168

Protein conservation

Species	Match	AA	Alignment
Human		1950	D	A	P	E	R	E	G	L	I	A	Y	V	M	S	E	N	F	S	R	P	L	G	P	P
mutated	all conserved	1950	D	A	P	E	R	E	G	L	I	A	Y	L	M	S	E	N	F	S	R	P	L	G	P
Ptroglodytes	all conserved	1951	D	A	P	E	R	E	G	L	I	A	Y	M	M	S	E	N	F	S	R	P	L	G	P
Mmulatta	all identical	1952	D	A	P	E	R	E	G	L	I	A	N	V	M	N	E	N	F	S	R	P	F	G	P
Fcatus	all identical	1954	D	A	P	E	Q	E	G	L	I	A	H	V	M	N	E	N	F	S	R	R	R	G	P
Mmusculus	all conserved	1954	D	A	P	E	R	E	G	L	I	A	Y	M	M	N	E	N	F	S	R	R	S	G	P
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	2016	CHAIN		lost
1772	2016	TOPO_DOM	Cytoplasmic	lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.828	0.94
	0.927	0.931
(flanking)	1.413	0.912

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

Strand

-1

Original gDNA sequence snippet

GAGAGGGCCTCATCGCCTACGTGATGAGTGAGAACTTCTCC

Altered gDNA sequence snippet

GAGAGGGCCTCATCGCCTACTTGATGAGTGAGAACTTCTCC

Original cDNA sequence snippet

GAGAGGGCCTCATCGCCTACGTGATGAGTGAGAACTTCTCC

Altered cDNA sequence snippet

GAGAGGGCCTCATCGCCTACTTGATGAGTGAGAACTTCTCC

Wildtype AA sequence

MANFLLPRGT SSFRRFTRES LAAIEKRMAE KQARGSTTLQ ESREGLPEEE APRPQLDLQA
SKKLPDLYGN PPQELIGEPL EDLDPFYSTQ KTFIVLNKGK TIFRFSATNA LYVLSPFHPI
RRAAVKILVH SLFNMLIMCT ILTNCVFMAQ HDPPPWTKYV EYTFTAIYTF ESLVKILARG
FCLHAFTFLR DPWNWLDFSV IIMAYTTEFV DLGNVSALRT FRVLRALKTI SVISGLKTIV
GALIQSVKKL ADVMVLTVFC LSVFALIGLQ LFMGNLRHKC VRNFTALNGT NGSVEADGLV
WESLDLYLSD PENYLLKNGT SDVLLCGNSS DAGTCPEGYR CLKAGENPDH GYTSFDSFAW
AFLALFRLMT QDCWERLYQQ TLRSAGKIYM IFFMLVIFLG SFYLVNLILA VVAMAYEEQN
QATIAETEEK EKRFQEAMEM LKKEHEALTI RGVDTVSRSS LEMSPLAPVN SHERRSKRRK
RMSSGTEECG EDRLPKSDSE DGPRAMNHLS LTRGLSRTSM KPRSSRGSIF TFRRRDLGSE
ADFADDENST AGESESHHTS LLVPWPLRRT SAQGQPSPGT SAPGHALHGK KNSTVDCNGV
VSLLGAGDPE ATSPGSHLLR PVMLEHPPDT TTPSEEPGGP QMLTSQAPCV DGFEEPGARQ
RALSAVSVLT SALEELEESR HKCPPCWNRL AQRYLIWECC PLWMSIKQGV KLVVMDPFTD
LTITMCIVLN TLFMALEHYN MTSEFEEMLQ VGNLVFTGIF TAEMTFKIIA LDPYYYFQQG
WNIFDSIIVI LSLMELGLSR MSNLSVLRSF RLLRVFKLAK SWPTLNTLIK IIGNSVGALG
NLTLVLAIIV FIFAVVGMQL FGKNYSELRD SDSGLLPRWH MMDFFHAFLI IFRILCGEWI
ETMWDCMEVS GQSLCLLVFL LVMVIGNLVV LNLFLALLLS SFSADNLTAP DEDREMNNLQ
LALARIQRGL RFVKRTTWDF CCGLLRQRPQ KPAALAAQGQ LPSCIATPYS PPPPETEKVP
PTRKETRFEE GEQPGQGTPG DPEPVCVPIA VAESDTDDQE EDEENSLGTE EESSKQESQP
VSGGPEAPPD SRTWSQVSAT ASSEAEASAS QADWRQQWKA EPQAPGCGET PEDSCSEGST
ADMTNTAELL EQIPDLGQDV KDPEDCFTEG CVRRCPCCAV DTTQAPGKVW WRLRKTCYHI
VEHSWFETFI IFMILLSSGA LAFEDIYLEE RKTIKVLLEY ADKMFTYVFV LEMLLKWVAY
GFKKYFTNAW CWLDFLIVDV SLVSLVANTL GFAEMGPIKS LRTLRALRPL RALSRFEGMR
VVVNALVGAI PSIMNVLLVC LIFWLIFSIM GVNLFAGKFG RCINQTEGDL PLNYTIVNNK
SQCESLNLTG ELYWTKVKVN FDNVGAGYLA LLQVATFKGW MDIMYAAVDS RGYEEQPQWE
YNLYMYIYFV IFIIFGSFFT LNLFIGVIID NFNQQKKKLG GQDIFMTEEQ KKYYNAMKKL
GSKKPQKPIP RPLNKYQGFI FDIVTKQAFD VTIMFLICLN MVTMMVETDD QSPEKINILA
KINLLFVAIF TGECIVKLAA LRHYYFTNSW NIFDFVVVIL SIVGTVLSDI IQKYFFSPTL
FRVIRLARIG RILRLIRGAK GIRTLLFALM MSLPALFNIG LLLFLVMFIY SIFGMANFAY
VKWEAGIDDM FNFQTFANSM LCLFQITTSA GWDGLLSPIL NTGPPYCDPT LPNSNGSRGD
CGSPAVGILF FTTYIIISFL IVVNMYIAII LENFSVATEE STEPLSEDDF DMFYEIWEKF
DPEATQFIEY SVLSDFADAL SEPLRIAKPN QISLINMDLP MVSGDRIHCM DILFAFTKRV
LGESGEMDAL KIQMEEKFMA ANPSKISYEP ITTTLRRKHE EVSAMVIQRA FRRHLLQRSL
KHASFLFRQQ AGSGLSEEDA PEREGLIAYV MSENFSRPLG PPSSSSISST SFPPSYDSVT
RATSDNLQVR GSDYSHSEDL ADFPPSPDRD RESIV*

Mutated AA sequence

MANFLLPRGT SSFRRFTRES LAAIEKRMAE KQARGSTTLQ ESREGLPEEE APRPQLDLQA
SKKLPDLYGN PPQELIGEPL EDLDPFYSTQ KTFIVLNKGK TIFRFSATNA LYVLSPFHPI
RRAAVKILVH SLFNMLIMCT ILTNCVFMAQ HDPPPWTKYV EYTFTAIYTF ESLVKILARG
FCLHAFTFLR DPWNWLDFSV IIMAYTTEFV DLGNVSALRT FRVLRALKTI SVISGLKTIV
GALIQSVKKL ADVMVLTVFC LSVFALIGLQ LFMGNLRHKC VRNFTALNGT NGSVEADGLV
WESLDLYLSD PENYLLKNGT SDVLLCGNSS DAGTCPEGYR CLKAGENPDH GYTSFDSFAW
AFLALFRLMT QDCWERLYQQ TLRSAGKIYM IFFMLVIFLG SFYLVNLILA VVAMAYEEQN
QATIAETEEK EKRFQEAMEM LKKEHEALTI RGVDTVSRSS LEMSPLAPVN SHERRSKRRK
RMSSGTEECG EDRLPKSDSE DGPRAMNHLS LTRGLSRTSM KPRSSRGSIF TFRRRDLGSE
ADFADDENST AGESESHHTS LLVPWPLRRT SAQGQPSPGT SAPGHALHGK KNSTVDCNGV
VSLLGAGDPE ATSPGSHLLR PVMLEHPPDT TTPSEEPGGP QMLTSQAPCV DGFEEPGARQ
RALSAVSVLT SALEELEESR HKCPPCWNRL AQRYLIWECC PLWMSIKQGV KLVVMDPFTD
LTITMCIVLN TLFMALEHYN MTSEFEEMLQ VGNLVFTGIF TAEMTFKIIA LDPYYYFQQG
WNIFDSIIVI LSLMELGLSR MSNLSVLRSF RLLRVFKLAK SWPTLNTLIK IIGNSVGALG
NLTLVLAIIV FIFAVVGMQL FGKNYSELRD SDSGLLPRWH MMDFFHAFLI IFRILCGEWI
ETMWDCMEVS GQSLCLLVFL LVMVIGNLVV LNLFLALLLS SFSADNLTAP DEDREMNNLQ
LALARIQRGL RFVKRTTWDF CCGLLRQRPQ KPAALAAQGQ LPSCIATPYS PPPPETEKVP
PTRKETRFEE GEQPGQGTPG DPEPVCVPIA VAESDTDDQE EDEENSLGTE EESSKQESQP
VSGGPEAPPD SRTWSQVSAT ASSEAEASAS QADWRQQWKA EPQAPGCGET PEDSCSEGST
ADMTNTAELL EQIPDLGQDV KDPEDCFTEG CVRRCPCCAV DTTQAPGKVW WRLRKTCYHI
VEHSWFETFI IFMILLSSGA LAFEDIYLEE RKTIKVLLEY ADKMFTYVFV LEMLLKWVAY
GFKKYFTNAW CWLDFLIVDV SLVSLVANTL GFAEMGPIKS LRTLRALRPL RALSRFEGMR
VVVNALVGAI PSIMNVLLVC LIFWLIFSIM GVNLFAGKFG RCINQTEGDL PLNYTIVNNK
SQCESLNLTG ELYWTKVKVN FDNVGAGYLA LLQVATFKGW MDIMYAAVDS RGYEEQPQWE
YNLYMYIYFV IFIIFGSFFT LNLFIGVIID NFNQQKKKLG GQDIFMTEEQ KKYYNAMKKL
GSKKPQKPIP RPLNKYQGFI FDIVTKQAFD VTIMFLICLN MVTMMVETDD QSPEKINILA
KINLLFVAIF TGECIVKLAA LRHYYFTNSW NIFDFVVVIL SIVGTVLSDI IQKYFFSPTL
FRVIRLARIG RILRLIRGAK GIRTLLFALM MSLPALFNIG LLLFLVMFIY SIFGMANFAY
VKWEAGIDDM FNFQTFANSM LCLFQITTSA GWDGLLSPIL NTGPPYCDPT LPNSNGSRGD
CGSPAVGILF FTTYIIISFL IVVNMYIAII LENFSVATEE STEPLSEDDF DMFYEIWEKF
DPEATQFIEY SVLSDFADAL SEPLRIAKPN QISLINMDLP MVSGDRIHCM DILFAFTKRV
LGESGEMDAL KIQMEEKFMA ANPSKISYEP ITTTLRRKHE EVSAMVIQRA FRRHLLQRSL
KHASFLFRQQ AGSGLSEEDA PEREGLIAYL MSENFSRPLG PPSSSSISST SFPPSYDSVT
RATSDNLQVR GSDYSHSEDL ADFPPSPDRD RESIV*

Position of stopcodon in wt / mu CDS

6048 / 6048

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

2016 / 2016

Position of stopcodon in wt / mu cDNA

6257 / 6257

Position of start ATG in wt / mu cDNA

210 / 210

Last intron/exon boundary

5019

Theoretical NMD boundary in CDS

4759

Length of CDS

6048

Coding sequence (CDS) position

5848

cDNA position

6057

gDNA position

99223

Chromosomal position

38550521

Speed

0.11 s

MutationT@ster 2025

Transcript summary:

MutationT@ster 2025

Variant:

3:38550521C>A_1_ENST00000413689

Prediction:

Summary:

MutationT@ster 2025

Variant:

3:38550521C>A_3_ENST00000455624

Prediction:

Summary:

MutationT@ster 2025

Variant:

3:38550521C>A_4_ENST00000450102

Prediction:

Summary:

MutationT@ster 2025

Variant:

3:38550521C>A_6_ENST00000333535

Prediction:

Summary:

MutationT@ster 2025

Variant:

3:38550521C>A_7_ENST00000327956

Prediction:

Summary:

MutationT@ster 2025

Variant:

3:38550521C>A_8_ENST00000414099

Prediction:

Summary:

MutationT@ster 2025

Variant:

3:38550521C>A_5_ENST00000449557

Prediction:

Summary:

MutationT@ster 2025

Variant:

3:38550521C>A_2_ENST00000423572

Prediction:

Summary: