MutationT@ster 2025

NEVER press reload or F5 - unless you want to start from the very beginning.
Input seems to be ok - now mapping the variant to the different transcripts...
Querying Taster for transcript #1: ENST00000655275
Querying Taster for transcript #2: ENST00000449082
Querying Taster for transcript #3: ENST00000643924
MT speed 0.18 s - this script 2.593308 s

Transcript summary:

Permalink

Transcript	Gene symbol	Prediction	Tree vote	Model	Splice site change	Variant type	Protein length	Features at a glance
ENST00000449082(MANE Select)	SCN10A	Benign	18\|82	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Protein features (might be) affected
ENST00000655275	SCN10A	Benign	31\|69	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed
ENST00000643924	SCN10A	Benign	33\|67	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed

MutationT@ster 2025

Variant:

3:38718792G>T_2_ENST00000449082

Back to summary table

Prediction:

BenignPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 18|82 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr3:38718792G>T (GRCh38)

Gene symbol

SCN10A

Gene constraints

LOEUF: 1.06, LOF (oe): 0.93, misssense (oe): 0.99, synonymous (oe): 1.04 ? (gnomAD)

Ensembl transcript ID

ENST00000449082.3

Genbank transcript ID

NM_006514 (exact from MANE), NM_001293307 (by similarity)

UniProt / AlphaMissense peptide

SCNAA_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.3542C>A
g.97495C>A

AA changes

AAE:	T1181K	?
Score:	78

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs150773437
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	0	4	4

Protein conservation

Species	Match	AA	Alignment
Human		1181	A	F	E	D	Y	Y	L	D	Q	K	P	T	V	K	A	L	L	E	Y	T	D	R	V	F
mutated	not conserved	1181	A	F	E	D	Y	Y	L	D	Q	K	P	K	V	K	A	L	L	E	Y	T	D	R	V
Ptroglodytes	all identical	1184	A	F	E	D	Y	Y	L	D	Q	K	P	T	V	K	A	L	L	E	Y	T	D	R	V
Mmulatta	all identical	1181	A	F	E	D	Y	Y	L	D	Q	K	P	T	V	K	A	L	L	E	Y	T	D	R	V
Fcatus	all identical	1181	A	F	E	D	Y	Y	L	D	Q	K	P	T	V	K	A	L	L	E	Y	T	D	R	V
Mmusculus	not conserved	1182	A	F	E	D	N	Y	L	E	E	K	P	R	V	K	S	V	L	E	Y	T	D	R	V
Ggallus	not conserved	5028												N	I	K	T	M	L	E	Y	A	D	K	I
Trubripes	not conserved	1160	A	F	E	D	I	Y	I	E	K	R	K	V	I	K	L	V	L	E	A	A	D	K	V
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

Start (aa)	End (aa)	Feature	Details
1	1956	CHAIN		lost
1140	1449	REPEAT	III	lost
1172	1184	TOPO_DOM	Extracellular	lost
1180	1207	HELIX		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-9.191	0
	-0.304	0
(flanking)	0.776	0.005

?

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

TTACCTGGACCAGAAGCCCACGGTGAAAGCTTTGCTGGAGT

Altered gDNA sequence snippet

TTACCTGGACCAGAAGCCCAAGGTGAAAGCTTTGCTGGAGT

Original cDNA sequence snippet

TTACCTGGACCAGAAGCCCACGGTGAAAGCTTTGCTGGAGT

Altered cDNA sequence snippet

TTACCTGGACCAGAAGCCCAAGGTGAAAGCTTTGCTGGAGT

Wildtype AA sequence

MEFPIGSLET NNFRRFTPES LVEIEKQIAA KQGTKKAREK HREQKDQEEK PRPQLDLKAC
NQLPKFYGEL PAELIGEPLE DLDPFYSTHR TFMVLNKGRT ISRFSATRAL WLFSPFNLIR
RTAIKVSVHS WFSLFITVTI LVNCVCMTRT DLPEKIEYVF TVIYTFEALI KILARGFCLN
EFTYLRDPWN WLDFSVITLA YVGTAIDLRG ISGLRTFRVL RALKTVSVIP GLKVIVGALI
HSVKKLADVT ILTIFCLSVF ALVGLQLFKG NLKNKCVKND MAVNETTNYS SHRKPDIYIN
KRGTSDPLLC GNGSDSGHCP DGYICLKTSD NPDFNYTSFD SFAWAFLSLF RLMTQDSWER
LYQQTLRTSG KIYMIFFVLV IFLGSFYLVN LILAVVTMAY EEQNQATTDE IEAKEKKFQE
ALEMLRKEQE VLAALGIDTT SLHSHNGSPL TSKNASERRH RIKPRVSEGS TEDNKSPRSD
PYNQRRMSFL GLASGKRRAS HGSVFHFRSP GRDISLPEGV TDDGVFPGDH ESHRGSLLLG
GGAGQQGPLP RSPLPQPSNP DSRHGEDEHQ PPPTSELAPG AVDVSAFDAG QKKTFLSAEY
LDEPFRAQRA MSVVSIITSV LEELEESEQK CPPCLTSLSQ KYLIWDCCPM WVKLKTILFG
LVTDPFAELT ITLCIVVNTI FMAMEHHGMS PTFEAMLQIG NIVFTIFFTA EMVFKIIAFD
PYYYFQKKWN IFDCIIVTVS LLELGVAKKG SLSVLRSFRL LRVFKLAKSW PTLNTLIKII
GNSVGALGNL TIILAIIVFV FALVGKQLLG ENYRNNRKNI SAPHEDWPRW HMHDFFHSFL
IVFRILCGEW IENMWACMEV GQKSICLILF LTVMVLGNLV VLNLFIALLL NSFSADNLTA
PEDDGEVNNL QVALARIQVF GHRTKQALCS FFSRSCPFPQ PKAEPELVVK LPLSSSKAEN
HIAANTARGS SGGLQAPRGP RDEHSDFIAN PTVWVSVPIA EGESDLDDLE DDGGEDAQSF
QQEVIPKGQQ EQLQQVERCG DHLTPRSPGT GTSSEDLAPS LGETWKDESV PQVPAEGVDD
TSSSEGSTVD CLDPEEILRK IPELADDLEE PDDCFTEGCI RHCPCCKLDT TKSPWDVGWQ
VRKTCYRIVE HSWFESFIIF MILLSSGSLA FEDYYLDQKP TVKALLEYTD RVFTFIFVFE
MLLKWVAYGF KKYFTNAWCW LDFLIVNISL ISLTAKILEY SEVAPIKALR TLRALRPLRA
LSRFEGMRVV VDALVGAIPS IMNVLLVCLI FWLIFSIMGV NLFAGKFWRC INYTDGEFSL
VPLSIVNNKS DCKIQNSTGS FFWVNVKVNF DNVAMGYLAL LQVATFKGWM DIMYAAVDSR
EVNMQPKWED NVYMYLYFVI FIIFGGFFTL NLFVGVIIDN FNQQKKKLGG QDIFMTEEQK
KYYNAMKKLG SKKPQKPIPR PLNKFQGFVF DIVTRQAFDI TIMVLICLNM ITMMVETDDQ
SEEKTKILGK INQFFVAVFT GECVMKMFAL RQYYFTNGWN VFDFIVVVLS IASLIFSAIL
KSLQSYFSPT LFRVIRLARI GRILRLIRAA KGIRTLLFAL MMSLPALFNI GLLLFLVMFI
YSIFGMSSFP HVRWEAGIDD MFNFQTFANS MLCLFQITTS AGWDGLLSPI LNTGPPYCDP
NLPNSNGTRG DCGSPAVGII FFTTYIIISF LIMVNMYIAV ILENFNVATE ESTEPLSEDD
FDMFYETWEK FDPEATQFIT FSALSDFADT LSGPLRIPKP NRNILIQMDL PLVPGDKIHC
LDILFAFTKN VLGESGELDS LKANMEEKFM ATNLSKSSYE PIATTLRWKQ EDISATVIQK
AYRSYVLHRS MALSNTPCVP RAEEEAASLP DEGFVAFTAN ENCVLPDKSE TASATSFPPS
YESVTRGLSD RVNMRTSSSI QNEDEATSME LIAPGP*

Mutated AA sequence

MEFPIGSLET NNFRRFTPES LVEIEKQIAA KQGTKKAREK HREQKDQEEK PRPQLDLKAC
NQLPKFYGEL PAELIGEPLE DLDPFYSTHR TFMVLNKGRT ISRFSATRAL WLFSPFNLIR
RTAIKVSVHS WFSLFITVTI LVNCVCMTRT DLPEKIEYVF TVIYTFEALI KILARGFCLN
EFTYLRDPWN WLDFSVITLA YVGTAIDLRG ISGLRTFRVL RALKTVSVIP GLKVIVGALI
HSVKKLADVT ILTIFCLSVF ALVGLQLFKG NLKNKCVKND MAVNETTNYS SHRKPDIYIN
KRGTSDPLLC GNGSDSGHCP DGYICLKTSD NPDFNYTSFD SFAWAFLSLF RLMTQDSWER
LYQQTLRTSG KIYMIFFVLV IFLGSFYLVN LILAVVTMAY EEQNQATTDE IEAKEKKFQE
ALEMLRKEQE VLAALGIDTT SLHSHNGSPL TSKNASERRH RIKPRVSEGS TEDNKSPRSD
PYNQRRMSFL GLASGKRRAS HGSVFHFRSP GRDISLPEGV TDDGVFPGDH ESHRGSLLLG
GGAGQQGPLP RSPLPQPSNP DSRHGEDEHQ PPPTSELAPG AVDVSAFDAG QKKTFLSAEY
LDEPFRAQRA MSVVSIITSV LEELEESEQK CPPCLTSLSQ KYLIWDCCPM WVKLKTILFG
LVTDPFAELT ITLCIVVNTI FMAMEHHGMS PTFEAMLQIG NIVFTIFFTA EMVFKIIAFD
PYYYFQKKWN IFDCIIVTVS LLELGVAKKG SLSVLRSFRL LRVFKLAKSW PTLNTLIKII
GNSVGALGNL TIILAIIVFV FALVGKQLLG ENYRNNRKNI SAPHEDWPRW HMHDFFHSFL
IVFRILCGEW IENMWACMEV GQKSICLILF LTVMVLGNLV VLNLFIALLL NSFSADNLTA
PEDDGEVNNL QVALARIQVF GHRTKQALCS FFSRSCPFPQ PKAEPELVVK LPLSSSKAEN
HIAANTARGS SGGLQAPRGP RDEHSDFIAN PTVWVSVPIA EGESDLDDLE DDGGEDAQSF
QQEVIPKGQQ EQLQQVERCG DHLTPRSPGT GTSSEDLAPS LGETWKDESV PQVPAEGVDD
TSSSEGSTVD CLDPEEILRK IPELADDLEE PDDCFTEGCI RHCPCCKLDT TKSPWDVGWQ
VRKTCYRIVE HSWFESFIIF MILLSSGSLA FEDYYLDQKP KVKALLEYTD RVFTFIFVFE
MLLKWVAYGF KKYFTNAWCW LDFLIVNISL ISLTAKILEY SEVAPIKALR TLRALRPLRA
LSRFEGMRVV VDALVGAIPS IMNVLLVCLI FWLIFSIMGV NLFAGKFWRC INYTDGEFSL
VPLSIVNNKS DCKIQNSTGS FFWVNVKVNF DNVAMGYLAL LQVATFKGWM DIMYAAVDSR
EVNMQPKWED NVYMYLYFVI FIIFGGFFTL NLFVGVIIDN FNQQKKKLGG QDIFMTEEQK
KYYNAMKKLG SKKPQKPIPR PLNKFQGFVF DIVTRQAFDI TIMVLICLNM ITMMVETDDQ
SEEKTKILGK INQFFVAVFT GECVMKMFAL RQYYFTNGWN VFDFIVVVLS IASLIFSAIL
KSLQSYFSPT LFRVIRLARI GRILRLIRAA KGIRTLLFAL MMSLPALFNI GLLLFLVMFI
YSIFGMSSFP HVRWEAGIDD MFNFQTFANS MLCLFQITTS AGWDGLLSPI LNTGPPYCDP
NLPNSNGTRG DCGSPAVGII FFTTYIIISF LIMVNMYIAV ILENFNVATE ESTEPLSEDD
FDMFYETWEK FDPEATQFIT FSALSDFADT LSGPLRIPKP NRNILIQMDL PLVPGDKIHC
LDILFAFTKN VLGESGELDS LKANMEEKFM ATNLSKSSYE PIATTLRWKQ EDISATVIQK
AYRSYVLHRS MALSNTPCVP RAEEEAASLP DEGFVAFTAN ENCVLPDKSE TASATSFPPS
YESVTRGLSD RVNMRTSSSI QNEDEATSME LIAPGP*

Position of stopcodon in wt / mu CDS

5871 / 5871

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

1957 / 1957

Position of stopcodon in wt / mu cDNA

6084 / 6084

Position of start ATG in wt / mu cDNA

214 / 214

Last intron/exon boundary

4870

Theoretical NMD boundary in CDS

4606

Length of CDS

5871

Coding sequence (CDS) position

3542

cDNA position

3755

gDNA position

97495

Chromosomal position

38718792

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

Back to summary table

MutationT@ster 2025

Variant:

3:38718792G>T_1_ENST00000655275

Back to summary table

Prediction:

BenignPermalink

Summary:

Amino acid sequence changed

Model: simple_aae
Tree vote: 31|69 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr3:38718792G>T (GRCh38)

Gene symbol

SCN10A

Gene constraints

LOEUF: 1.05, LOF (oe): 0.92, misssense (oe): 0.99, synonymous (oe): 1.03 ? (gnomAD)

Ensembl transcript ID

ENST00000655275.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.3566C>A
g.97495C>A

AA changes

AAE:	T1189K	?
Score:	78

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs150773437
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	0	4	4

Protein conservation

Species	Match	AA	Alignment
Human		1189	A	F	E	D	Y	Y	L	D	Q	K	P	T	V	K	A	L	L	E	Y	T	D	R	V	F
mutated	not conserved	1189	A	F	E	D	Y	Y	L	D	Q	K	P	K	V	K	A	L	L	E	Y	T	D	R	V
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)	-9.191	0
	-0.304	0
(flanking)	0.776	0.005

?

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

TTACCTGGACCAGAAGCCCACGGTGAAAGCTTTGCTGGAGT

Altered gDNA sequence snippet

TTACCTGGACCAGAAGCCCAAGGTGAAAGCTTTGCTGGAGT

Original cDNA sequence snippet

TTACCTGGACCAGAAGCCCACGGTGAAAGCTTTGCTGGAGT

Altered cDNA sequence snippet

TTACCTGGACCAGAAGCCCAAGGTGAAAGCTTTGCTGGAGT

Wildtype AA sequence

MEFPIGSLET NNFRRFTPES LVEIEKQIAA KQGTKKAREK HREQKDQEEK PRPQLDLKAC
NQLPKFYGEL PAELIGEPLE DLDPFYSTHR TFMVLNKGRT ISRFSATRAL WLFSPFNLIR
RTAIKVSVHS WFSLFITVTI LVNCVCMTRT DLPEKIEYVF TVIYTFEALI KILARGFCLN
EFTYLRDPWN WLDFSVITLA YVGTAIDLRG ISGLRTFRVL RALKTVSVIP GLKVIVGALI
HSVKKLADVT ILTIFCLSVF ALVGLQLFKG NLKNKCVKND MAVNETTNYS SHRKREWSLF
HRDQDIYINK RGTSDPLLCG NGSDSGHCPD GYICLKTSDN PDFNYTSFDS FAWAFLSLFR
LMTQDSWERL YQQTLRTSGK IYMIFFVLVI FLGSFYLVNL ILAVVTMAYE EQNQATTDEI
EAKEKKFQEA LEMLRKEQEV LAALGIDTTS LHSHNGSPLT SKNASERRHR IKPRVSEGST
EDNKSPRSDP YNQRRMSFLG LASGKRRASH GSVFHFRSPG RDISLPEGVT DDGVFPGDHE
SHRGSLLLGG GAGQQGPLPR SPLPQPSNPD SRHGEDEHQP PPTSELAPGA VDVSAFDAGQ
KKTFLSAEYL DEPFRAQRAM SVVSIITSVL EELEESEQKC PPCLTSLSQK YLIWDCCPMW
VKLKTILFGL VTDPFAELTI TLCIVVNTIF MAMEHHGMSP TFEAMLQIGN IVFTIFFTAE
MVFKIIAFDP YYYFQKKWNI FDCIIVTVSL LELGVAKKGS LSVLRSFRLL RVFKLAKSWP
TLNTLIKIIG NSVGALGNLT IILAIIVFVF ALVGKQLLGE NYRNNRKNIS APHEDWPRWH
MHDFFHSFLI VFRILCGEWI ENMWACMEVG QKSICLILFL TVMVLGNLVV LNLFIALLLN
SFSADNLTAP EDDGEVNNLQ VALARIQVFG HRTKQALCSF FSRSCPFPQP KAEPELVVKL
PLSSSKAENH IAANTARGSS GGLQAPRGPR DEHSDFIANP TVWVSVPIAE GESDLDDLED
DGGEDAQSFQ QEVIPKGQEQ LQQVERCGDH LTPRSPGTGT SSEDLAPSLG ETWKDESVPQ
VPAEGVDDTS SSEGSTVDCL DPEEILRKIP ELADDLEEPD DCFTEGCIRH CPCCKLDTTK
SPWDVGWQVR KTCYRIVEHS WFESFIIFMI LLSSGSLAFE DYYLDQKPTV KALLEYTDRV
FTFIFVFEML LKWVAYGFKK YFTNAWCWLD FLIVNISLIS LTAKILEYSE VAPIKALRTL
RALRPLRALS RFEGMRVVVD ALVGAIPSIM NVLLVCLIFW LIFSIMGVNL FAGKFWRCIN
YTDGEFSLVP LSIVNNKSDC KIQNSTGSFF WVNVKVNFDN VAMGYLALLQ VATFKGWMDI
MYAAVDSREV NMQPKWEDNV YMYLYFVIFI IFGGFFTLNL FVGVIIDNFN QQKKKLGGQD
IFMTEEQKKY YNAMKKLGSK KPQKPIPRPL NKFQGFVFDI VTRQAFDITI MVLICLNMIT
MMVETDDQSE EKTKILGKIN QFFVAVFTGE CVMKMFALRQ YYFTNGWNVF DFIVVVLSIA
SLIFSAILKS LQSYFSPTLF RVIRLARIGR ILRLIRAAKG IRTLLFALMM SLPALFNIGL
LLFLVMFIYS IFGMSSFPHV RWEAGIDDMF NFQTFANSML CLFQITTSAG WDGLLSPILN
TGPPYCDPNL PNSNGTRGDC GSPAVGIIFF TTYIIISFLI MVNMYIAVIL ENFNVATEES
TEPLSEDDFD MFYETWEKFD PEATQFITFS ALSDFADTLS GPLRIPKPNR NILIQMDLPL
VPGDKIHCLD ILFAFTKNVL GESGELDSLK ANMEEKFMAT NLSKSSYEPI ATTLRWKQED
ISATVIQKAY RSYVLHRSMA LSNTPCVPRA EEEAASLPDE GFVAFTANEN CVLPDKSETA
SATSFPPSYE SVTRGLSDRV NMRTSSSIQN EDEATSMELI APGP*

Mutated AA sequence

MEFPIGSLET NNFRRFTPES LVEIEKQIAA KQGTKKAREK HREQKDQEEK PRPQLDLKAC
NQLPKFYGEL PAELIGEPLE DLDPFYSTHR TFMVLNKGRT ISRFSATRAL WLFSPFNLIR
RTAIKVSVHS WFSLFITVTI LVNCVCMTRT DLPEKIEYVF TVIYTFEALI KILARGFCLN
EFTYLRDPWN WLDFSVITLA YVGTAIDLRG ISGLRTFRVL RALKTVSVIP GLKVIVGALI
HSVKKLADVT ILTIFCLSVF ALVGLQLFKG NLKNKCVKND MAVNETTNYS SHRKREWSLF
HRDQDIYINK RGTSDPLLCG NGSDSGHCPD GYICLKTSDN PDFNYTSFDS FAWAFLSLFR
LMTQDSWERL YQQTLRTSGK IYMIFFVLVI FLGSFYLVNL ILAVVTMAYE EQNQATTDEI
EAKEKKFQEA LEMLRKEQEV LAALGIDTTS LHSHNGSPLT SKNASERRHR IKPRVSEGST
EDNKSPRSDP YNQRRMSFLG LASGKRRASH GSVFHFRSPG RDISLPEGVT DDGVFPGDHE
SHRGSLLLGG GAGQQGPLPR SPLPQPSNPD SRHGEDEHQP PPTSELAPGA VDVSAFDAGQ
KKTFLSAEYL DEPFRAQRAM SVVSIITSVL EELEESEQKC PPCLTSLSQK YLIWDCCPMW
VKLKTILFGL VTDPFAELTI TLCIVVNTIF MAMEHHGMSP TFEAMLQIGN IVFTIFFTAE
MVFKIIAFDP YYYFQKKWNI FDCIIVTVSL LELGVAKKGS LSVLRSFRLL RVFKLAKSWP
TLNTLIKIIG NSVGALGNLT IILAIIVFVF ALVGKQLLGE NYRNNRKNIS APHEDWPRWH
MHDFFHSFLI VFRILCGEWI ENMWACMEVG QKSICLILFL TVMVLGNLVV LNLFIALLLN
SFSADNLTAP EDDGEVNNLQ VALARIQVFG HRTKQALCSF FSRSCPFPQP KAEPELVVKL
PLSSSKAENH IAANTARGSS GGLQAPRGPR DEHSDFIANP TVWVSVPIAE GESDLDDLED
DGGEDAQSFQ QEVIPKGQEQ LQQVERCGDH LTPRSPGTGT SSEDLAPSLG ETWKDESVPQ
VPAEGVDDTS SSEGSTVDCL DPEEILRKIP ELADDLEEPD DCFTEGCIRH CPCCKLDTTK
SPWDVGWQVR KTCYRIVEHS WFESFIIFMI LLSSGSLAFE DYYLDQKPKV KALLEYTDRV
FTFIFVFEML LKWVAYGFKK YFTNAWCWLD FLIVNISLIS LTAKILEYSE VAPIKALRTL
RALRPLRALS RFEGMRVVVD ALVGAIPSIM NVLLVCLIFW LIFSIMGVNL FAGKFWRCIN
YTDGEFSLVP LSIVNNKSDC KIQNSTGSFF WVNVKVNFDN VAMGYLALLQ VATFKGWMDI
MYAAVDSREV NMQPKWEDNV YMYLYFVIFI IFGGFFTLNL FVGVIIDNFN QQKKKLGGQD
IFMTEEQKKY YNAMKKLGSK KPQKPIPRPL NKFQGFVFDI VTRQAFDITI MVLICLNMIT
MMVETDDQSE EKTKILGKIN QFFVAVFTGE CVMKMFALRQ YYFTNGWNVF DFIVVVLSIA
SLIFSAILKS LQSYFSPTLF RVIRLARIGR ILRLIRAAKG IRTLLFALMM SLPALFNIGL
LLFLVMFIYS IFGMSSFPHV RWEAGIDDMF NFQTFANSML CLFQITTSAG WDGLLSPILN
TGPPYCDPNL PNSNGTRGDC GSPAVGIIFF TTYIIISFLI MVNMYIAVIL ENFNVATEES
TEPLSEDDFD MFYETWEKFD PEATQFITFS ALSDFADTLS GPLRIPKPNR NILIQMDLPL
VPGDKIHCLD ILFAFTKNVL GESGELDSLK ANMEEKFMAT NLSKSSYEPI ATTLRWKQED
ISATVIQKAY RSYVLHRSMA LSNTPCVPRA EEEAASLPDE GFVAFTANEN CVLPDKSETA
SATSFPPSYE SVTRGLSDRV NMRTSSSIQN EDEATSMELI APGP*

Position of stopcodon in wt / mu CDS

5895 / 5895

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

1965 / 1965

Position of stopcodon in wt / mu cDNA

6157 / 6157

Position of start ATG in wt / mu cDNA

263 / 263

Last intron/exon boundary

4943

Theoretical NMD boundary in CDS

4630

Length of CDS

5895

Coding sequence (CDS) position

3566

cDNA position

3828

gDNA position

97495

Chromosomal position

38718792

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

Back to summary table

MutationT@ster 2025

Variant:

3:38718792G>T_3_ENST00000643924

Back to summary table

Prediction:

BenignPermalink

Summary:

Amino acid sequence changed

Model: simple_aae
Tree vote: 33|67 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr3:38718792G>T (GRCh38)

Gene symbol

SCN10A

Gene constraints

LOEUF: 1.06, LOF (oe): 0.92, misssense (oe): 0.99, synonymous (oe): 1.03 ? (gnomAD)

Ensembl transcript ID

ENST00000643924.1

Genbank transcript ID

NM_001293306 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.3539C>A
g.97495C>A

AA changes

AAE:	T1180K	?
Score:	78

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs150773437
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	0	4	4

Protein conservation

Species	Match	AA	Alignment
Human		1180	A	F	E	D	Y	Y	L	D	Q	K	P	T	V	K	A	L	L	E	Y	T	D	R	V	F
mutated	not conserved	1180	A	F	E	D	Y	Y	L	D	Q	K	P	K	V	K	A	L	L	E	Y	T	D	R	V
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)	-9.191	0
	-0.304	0
(flanking)	0.776	0.005

?

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

TTACCTGGACCAGAAGCCCACGGTGAAAGCTTTGCTGGAGT

Altered gDNA sequence snippet

TTACCTGGACCAGAAGCCCAAGGTGAAAGCTTTGCTGGAGT

Original cDNA sequence snippet

TTACCTGGACCAGAAGCCCACGGTGAAAGCTTTGCTGGAGT

Altered cDNA sequence snippet

TTACCTGGACCAGAAGCCCAAGGTGAAAGCTTTGCTGGAGT

Wildtype AA sequence

MEFPIGSLET NNFRRFTPES LVEIEKQIAA KQGTKKAREK HREQKDQEEK PRPQLDLKAC
NQLPKFYGEL PAELIGEPLE DLDPFYSTHR TFMVLNKGRT ISRFSATRAL WLFSPFNLIR
RTAIKVSVHS WFSLFITVTI LVNCVCMTRT DLPEKIEYVF TVIYTFEALI KILARGFCLN
EFTYLRDPWN WLDFSVITLA YVGTAIDLRG ISGLRTFRVL RALKTVSVIP GLKVIVGALI
HSVKKLADVT ILTIFCLSVF ALVGLQLFKG NLKNKCVKND MAVNETTNYS SHRKPDIYIN
KRGTSDPLLC GNGSDSGHCP DGYICLKTSD NPDFNYTSFD SFAWAFLSLF RLMTQDSWER
LYQQTLRTSG KIYMIFFVLV IFLGSFYLVN LILAVVTMAY EEQNQATTDE IEAKEKKFQE
ALEMLRKEQE VLAALGIDTT SLHSHNGSPL TSKNASERRH RIKPRVSEGS TEDNKSPRSD
PYNQRRMSFL GLASGKRRAS HGSVFHFRSP GRDISLPEGV TDDGVFPGDH ESHRGSLLLG
GGAGQQGPLP RSPLPQPSNP DSRHGEDEHQ PPPTSELAPG AVDVSAFDAG QKKTFLSAEY
LDEPFRAQRA MSVVSIITSV LEELEESEQK CPPCLTSLSQ KYLIWDCCPM WVKLKTILFG
LVTDPFAELT ITLCIVVNTI FMAMEHHGMS PTFEAMLQIG NIVFTIFFTA EMVFKIIAFD
PYYYFQKKWN IFDCIIVTVS LLELGVAKKG SLSVLRSFRL LRVFKLAKSW PTLNTLIKII
GNSVGALGNL TIILAIIVFV FALVGKQLLG ENYRNNRKNI SAPHEDWPRW HMHDFFHSFL
IVFRILCGEW IENMWACMEV GQKSICLILF LTVMVLGNLV VLNLFIALLL NSFSADNLTA
PEDDGEVNNL QVALARIQVF GHRTKQALCS FFSRSCPFPQ PKAEPELVVK LPLSSSKAEN
HIAANTARGS SGGLQAPRGP RDEHSDFIAN PTVWVSVPIA EGESDLDDLE DDGGEDAQSF
QQEVIPKGQE QLQQVERCGD HLTPRSPGTG TSSEDLAPSL GETWKDESVP QVPAEGVDDT
SSSEGSTVDC LDPEEILRKI PELADDLEEP DDCFTEGCIR HCPCCKLDTT KSPWDVGWQV
RKTCYRIVEH SWFESFIIFM ILLSSGSLAF EDYYLDQKPT VKALLEYTDR VFTFIFVFEM
LLKWVAYGFK KYFTNAWCWL DFLIVNISLI SLTAKILEYS EVAPIKALRT LRALRPLRAL
SRFEGMRVVV DALVGAIPSI MNVLLVCLIF WLIFSIMGVN LFAGKFWRCI NYTDGEFSLV
PLSIVNNKSD CKIQNSTGSF FWVNVKVNFD NVAMGYLALL QVATFKGWMD IMYAAVDSRE
VNMQPKWEDN VYMYLYFVIF IIFGGFFTLN LFVGVIIDNF NQQKKKLGGQ DIFMTEEQKK
YYNAMKKLGS KKPQKPIPRP LNKFQGFVFD IVTRQAFDIT IMVLICLNMI TMMVETDDQS
EEKTKILGKI NQFFVAVFTG ECVMKMFALR QYYFTNGWNV FDFIVVVLSI ASLIFSAILK
SLQSYFSPTL FRVIRLARIG RILRLIRAAK GIRTLLFALM MSLPALFNIG LLLFLVMFIY
SIFGMSSFPH VRWEAGIDDM FNFQTFANSM LCLFQITTSA GWDGLLSPIL NTGPPYCDPN
LPNSNGTRGD CGSPAVGIIF FTTYIIISFL IMVNMYIAVI LENFNVATEE STEPLSEDDF
DMFYETWEKF DPEATQFITF SALSDFADTL SGPLRIPKPN RNILIQMDLP LVPGDKIHCL
DILFAFTKNV LGESGELDSL KANMEEKFMA TNLSKSSYEP IATTLRWKQE DISATVIQKA
YRSYVLHRSM ALSNTPCVPR AEEEAASLPD EGFVAFTANE NCVLPDKSET ASATSFPPSY
ESVTRGLSDR VNMRTSSSIQ NEDEATSMEL IAPGP*

Mutated AA sequence

MEFPIGSLET NNFRRFTPES LVEIEKQIAA KQGTKKAREK HREQKDQEEK PRPQLDLKAC
NQLPKFYGEL PAELIGEPLE DLDPFYSTHR TFMVLNKGRT ISRFSATRAL WLFSPFNLIR
RTAIKVSVHS WFSLFITVTI LVNCVCMTRT DLPEKIEYVF TVIYTFEALI KILARGFCLN
EFTYLRDPWN WLDFSVITLA YVGTAIDLRG ISGLRTFRVL RALKTVSVIP GLKVIVGALI
HSVKKLADVT ILTIFCLSVF ALVGLQLFKG NLKNKCVKND MAVNETTNYS SHRKPDIYIN
KRGTSDPLLC GNGSDSGHCP DGYICLKTSD NPDFNYTSFD SFAWAFLSLF RLMTQDSWER
LYQQTLRTSG KIYMIFFVLV IFLGSFYLVN LILAVVTMAY EEQNQATTDE IEAKEKKFQE
ALEMLRKEQE VLAALGIDTT SLHSHNGSPL TSKNASERRH RIKPRVSEGS TEDNKSPRSD
PYNQRRMSFL GLASGKRRAS HGSVFHFRSP GRDISLPEGV TDDGVFPGDH ESHRGSLLLG
GGAGQQGPLP RSPLPQPSNP DSRHGEDEHQ PPPTSELAPG AVDVSAFDAG QKKTFLSAEY
LDEPFRAQRA MSVVSIITSV LEELEESEQK CPPCLTSLSQ KYLIWDCCPM WVKLKTILFG
LVTDPFAELT ITLCIVVNTI FMAMEHHGMS PTFEAMLQIG NIVFTIFFTA EMVFKIIAFD
PYYYFQKKWN IFDCIIVTVS LLELGVAKKG SLSVLRSFRL LRVFKLAKSW PTLNTLIKII
GNSVGALGNL TIILAIIVFV FALVGKQLLG ENYRNNRKNI SAPHEDWPRW HMHDFFHSFL
IVFRILCGEW IENMWACMEV GQKSICLILF LTVMVLGNLV VLNLFIALLL NSFSADNLTA
PEDDGEVNNL QVALARIQVF GHRTKQALCS FFSRSCPFPQ PKAEPELVVK LPLSSSKAEN
HIAANTARGS SGGLQAPRGP RDEHSDFIAN PTVWVSVPIA EGESDLDDLE DDGGEDAQSF
QQEVIPKGQE QLQQVERCGD HLTPRSPGTG TSSEDLAPSL GETWKDESVP QVPAEGVDDT
SSSEGSTVDC LDPEEILRKI PELADDLEEP DDCFTEGCIR HCPCCKLDTT KSPWDVGWQV
RKTCYRIVEH SWFESFIIFM ILLSSGSLAF EDYYLDQKPK VKALLEYTDR VFTFIFVFEM
LLKWVAYGFK KYFTNAWCWL DFLIVNISLI SLTAKILEYS EVAPIKALRT LRALRPLRAL
SRFEGMRVVV DALVGAIPSI MNVLLVCLIF WLIFSIMGVN LFAGKFWRCI NYTDGEFSLV
PLSIVNNKSD CKIQNSTGSF FWVNVKVNFD NVAMGYLALL QVATFKGWMD IMYAAVDSRE
VNMQPKWEDN VYMYLYFVIF IIFGGFFTLN LFVGVIIDNF NQQKKKLGGQ DIFMTEEQKK
YYNAMKKLGS KKPQKPIPRP LNKFQGFVFD IVTRQAFDIT IMVLICLNMI TMMVETDDQS
EEKTKILGKI NQFFVAVFTG ECVMKMFALR QYYFTNGWNV FDFIVVVLSI ASLIFSAILK
SLQSYFSPTL FRVIRLARIG RILRLIRAAK GIRTLLFALM MSLPALFNIG LLLFLVMFIY
SIFGMSSFPH VRWEAGIDDM FNFQTFANSM LCLFQITTSA GWDGLLSPIL NTGPPYCDPN
LPNSNGTRGD CGSPAVGIIF FTTYIIISFL IMVNMYIAVI LENFNVATEE STEPLSEDDF
DMFYETWEKF DPEATQFITF SALSDFADTL SGPLRIPKPN RNILIQMDLP LVPGDKIHCL
DILFAFTKNV LGESGELDSL KANMEEKFMA TNLSKSSYEP IATTLRWKQE DISATVIQKA
YRSYVLHRSM ALSNTPCVPR AEEEAASLPD EGFVAFTANE NCVLPDKSET ASATSFPPSY
ESVTRGLSDR VNMRTSSSIQ NEDEATSMEL IAPGP*

Position of stopcodon in wt / mu CDS

5868 / 5868

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

1956 / 1956

Position of stopcodon in wt / mu cDNA

5900 / 5900

Position of start ATG in wt / mu cDNA

33 / 33

Last intron/exon boundary

4686

Theoretical NMD boundary in CDS

4603

Length of CDS

5868

Coding sequence (CDS) position

3539

cDNA position

3571

gDNA position

97495

Chromosomal position

38718792

Speed

0.07 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

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