MutationT @ ster 2025

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Known disease mutation: ClinVar ID 5430 (pathogenic)
Protein features (might be) affected

Model: simple_aae
Tree vote: 97|3 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr10:93797277A>C (GRCh38)

Gene symbol

Gene constraints

LOEUF: 0.33, LOF (oe): 0.19, misssense (oe): 0.62, synonymous (oe): 0.87 ? (gnomAD)

Ensembl transcript ID

ENST00000371418.9

Genbank transcript ID

NM_005097 (exact from MANE)

UniProt / AlphaMissense peptide

LGI1_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.1148A>C
g.39438A>C

AA changes

AAE:	E383A	?
Score:	107

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Epilepsy, familial temporal lobe, 1

pathogenic

Variant DBs

	Not in dbSNP
	Allele 'C' was not found in gnomAD

Protein conservation

Species	Match	AA	Alignment
Human		383	S	L	H	A	W	Y	R	D	T	D	V	E	Y	L	E	I	V	R	T	P	Q	T	L	R
mutated	not conserved	383	S	L	H	A	W	Y	R	D	T	D	V	A	Y	L	E	I	V	R	T	P	Q	T	L
Ptroglodytes	all identical	383	S	L	H	A	W	Y	R	D	T	D	V	E	Y	L	E	I	V	R	T	P	Q	T	L
Mmulatta	all identical	383	S	L	H	A	W	Y	R	D	T	D	V	E	Y	L	E	I	V	R	T	P	Q	T	L
Fcatus	all identical	383	S	L	H	A	W	Y	R	D	T	D	V	E	Y	L	E	I	A	R	T	P	Q	T	L
Mmusculus	all identical	383	S	L	H	A	W	Y	R	D	T	D	V	E	Y	L	E	I	A	R	P	P	L	A	L
Ggallus	all identical	375	S	L	H	A	W	Y	R	D	T	D	V	E	F	L	E	I	A	-	-	-	-	-	-
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	all identical	378	S	V	H	A	W	Y	R	D	T	D	V	E	F	L	E	M	T	-	-	-	-	-	-

Protein features

Start (aa)	End (aa)	Feature	Details
35	557	CHAIN		lost
366	415	REPEAT	EAR	lost
379	387	STRAND		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	10.003	1
	9.325	1
(flanking)	3.276	1

?

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

10

Strand

1

Original gDNA sequence snippet

GTACAGGGACACTGATGTGGAATATCTAGAAATAGTCAGAA

Altered gDNA sequence snippet

GTACAGGGACACTGATGTGGCATATCTAGAAATAGTCAGAA

Original cDNA sequence snippet

GTACAGGGACACTGATGTGGAATATCTAGAAATAGTCAGAA

Altered cDNA sequence snippet

GTACAGGGACACTGATGTGGCATATCTAGAAATAGTCAGAA

Wildtype AA sequence

MESERSKRMG NACIPLKRIA YFLCLLSALL LTEGKKPAKP KCPAVCTCTK DNALCENARS
IPRTVPPDVI SLSFVRSGFT EISEGSFLFT PSLQLLLFTS NSFDVISDDA FIGLPHLEYL
FIENNNIKSI SRHTFRGLKS LIHLSLANNN LQTLPKDIFK GLDSLTNVDL RGNSFNCDCK
LKWLVEWLGH TNATVEDIYC EGPPEYKKRK INSLSSKDFD CIITEFAKSQ DLPYQSLSID
TFSYLNDEYV VIAQPFTGKC IFLEWDHVEK TFRNYDNITG TSTVVCKPIV IETQLYVIVA
QLFGGSHIYK RDSFANKFIK IQDIEILKIR KPNDIETFKI ENNWYFVVAD SSKAGFTTIY
KWNGNGFYSH QSLHAWYRDT DVEYLEIVRT PQTLRTPHLI LSSSSQRPVI YQWNKATQLF
TNQTDIPNME DVYAVKHFSV KGDVYICLTR FIGDSKVMKW GGSSFQDIQR MPSRGSMVFQ
PLQINNYQYA ILGSDYSFTQ VYNWDAEKAK FVKFQELNVQ APRSFTHVSI NKRNFLFASS
FKGNTQIYKH VIVDLSA*

Mutated AA sequence

MESERSKRMG NACIPLKRIA YFLCLLSALL LTEGKKPAKP KCPAVCTCTK DNALCENARS
IPRTVPPDVI SLSFVRSGFT EISEGSFLFT PSLQLLLFTS NSFDVISDDA FIGLPHLEYL
FIENNNIKSI SRHTFRGLKS LIHLSLANNN LQTLPKDIFK GLDSLTNVDL RGNSFNCDCK
LKWLVEWLGH TNATVEDIYC EGPPEYKKRK INSLSSKDFD CIITEFAKSQ DLPYQSLSID
TFSYLNDEYV VIAQPFTGKC IFLEWDHVEK TFRNYDNITG TSTVVCKPIV IETQLYVIVA
QLFGGSHIYK RDSFANKFIK IQDIEILKIR KPNDIETFKI ENNWYFVVAD SSKAGFTTIY
KWNGNGFYSH QSLHAWYRDT DVAYLEIVRT PQTLRTPHLI LSSSSQRPVI YQWNKATQLF
TNQTDIPNME DVYAVKHFSV KGDVYICLTR FIGDSKVMKW GGSSFQDIQR MPSRGSMVFQ
PLQINNYQYA ILGSDYSFTQ VYNWDAEKAK FVKFQELNVQ APRSFTHVSI NKRNFLFASS
FKGNTQIYKH VIVDLSA*

Position of stopcodon in wt / mu CDS

1674 / 1674

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

558 / 558

Position of stopcodon in wt / mu cDNA

1883 / 1883

Position of start ATG in wt / mu cDNA

210 / 210

Last intron/exon boundary

1047

Theoretical NMD boundary in CDS

787

Length of CDS

1674

Coding sequence (CDS) position

1148

cDNA position

1357

gDNA position

39438

Chromosomal position

93797277

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

MutationT@ster 2025

Variant:

10:93797277A>C_2_ENST00000629035

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Known disease mutation: ClinVar ID 5430 (pathogenic)

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

Analysed issue

Analysis result

Variant

Chr10:93797277A>C (GRCh38)

Gene symbol

Gene constraints

LOEUF: 0.33, LOF (oe): 0.20, misssense (oe): 0.62, synonymous (oe): 0.87 ? (gnomAD)

Ensembl transcript ID

ENST00000629035.2

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.1076A>C
g.39438A>C

AA changes

AAE:	E359A	?
Score:	107

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Epilepsy, familial temporal lobe, 1

pathogenic

Variant DBs

	Not in dbSNP
	Allele 'C' was not found in gnomAD

Protein conservation

Species	Match	AA	Alignment
Human		359	S	L	H	A	W	Y	R	D	T	D	V	E	Y	L	E	I	V	R	T	P	Q	T	L	R
mutated	not conserved	359	S	L	H	A	W	Y	R	D	T	D	V	A	Y	L	E	I	V	R	T	P	Q	T	L
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)	10.003	1
	9.325	1
(flanking)	3.276	1

?

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

10

Strand

1

Original gDNA sequence snippet

GTACAGGGACACTGATGTGGAATATCTAGAAATAGTCAGAA

Altered gDNA sequence snippet

GTACAGGGACACTGATGTGGCATATCTAGAAATAGTCAGAA

Original cDNA sequence snippet

GTACAGGGACACTGATGTGGAATATCTAGAAATAGTCAGAA

Altered cDNA sequence snippet

GTACAGGGACACTGATGTGGCATATCTAGAAATAGTCAGAA

Wildtype AA sequence

MESERSKRMG NACIPLKRIA YFLCLLSALL LTEGKKPAKP KCPAVCTCTK DNALCENARS
IPRTVPPDVI SLLFTSNSFD VISDDAFIGL PHLEYLFIEN NNIKSISRHT FRGLKSLIHL
SLANNNLQTL PKDIFKGLDS LTNVDLRGNS FNCDCKLKWL VEWLGHTNAT VEDIYCEGPP
EYKKRKINSL SSKDFDCIIT EFAKSQDLPY QSLSIDTFSY LNDEYVVIAQ PFTGKCIFLE
WDHVEKTFRN YDNITGTSTV VCKPIVIETQ LYVIVAQLFG GSHIYKRDSF ANKFIKIQDI
EILKIRKPND IETFKIENNW YFVVADSSKA GFTTIYKWNG NGFYSHQSLH AWYRDTDVEY
LEIVRTPQTL RTPHLILSSS SQRPVIYQWN KATQLFTNQT DIPNMEDVYA VKHFSVKGDV
YICLTRFIGD SKVMKWGGSS FQDIQRMPSR GSMVFQPLQI NNYQYAILGS DYSFTQVYNW
DAEKAKFVKF QELNVQAPRS FTHVSINKRN FLFASSFKGN TQIYKHVIVD LSA*

Mutated AA sequence

MESERSKRMG NACIPLKRIA YFLCLLSALL LTEGKKPAKP KCPAVCTCTK DNALCENARS
IPRTVPPDVI SLLFTSNSFD VISDDAFIGL PHLEYLFIEN NNIKSISRHT FRGLKSLIHL
SLANNNLQTL PKDIFKGLDS LTNVDLRGNS FNCDCKLKWL VEWLGHTNAT VEDIYCEGPP
EYKKRKINSL SSKDFDCIIT EFAKSQDLPY QSLSIDTFSY LNDEYVVIAQ PFTGKCIFLE
WDHVEKTFRN YDNITGTSTV VCKPIVIETQ LYVIVAQLFG GSHIYKRDSF ANKFIKIQDI
EILKIRKPND IETFKIENNW YFVVADSSKA GFTTIYKWNG NGFYSHQSLH AWYRDTDVAY
LEIVRTPQTL RTPHLILSSS SQRPVIYQWN KATQLFTNQT DIPNMEDVYA VKHFSVKGDV
YICLTRFIGD SKVMKWGGSS FQDIQRMPSR GSMVFQPLQI NNYQYAILGS DYSFTQVYNW
DAEKAKFVKF QELNVQAPRS FTHVSINKRN FLFASSFKGN TQIYKHVIVD LSA*

Position of stopcodon in wt / mu CDS

1602 / 1602

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

534 / 534

Position of stopcodon in wt / mu cDNA

1896 / 1896

Position of start ATG in wt / mu cDNA

295 / 295

Last intron/exon boundary

1060

Theoretical NMD boundary in CDS

715

Length of CDS

1602

Coding sequence (CDS) position

1076

cDNA position

1370

gDNA position

39438

Chromosomal position

93797277

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

MutationT@ster 2025

Variant:

10:93797277A>C_3_ENST00000630047

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Known disease mutation: ClinVar ID 5430 (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

Chr10:93797277A>C (GRCh38)

Gene symbol

Gene constraints

LOEUF: 0.30, LOF (oe): 0.17, misssense (oe): 0.63, synonymous (oe): 0.88 ? (gnomAD)

Ensembl transcript ID

ENST00000630047.2

Genbank transcript ID

NM_001308276 (by similarity)

UniProt / AlphaMissense peptide

LGI1_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.1004A>C
g.39438A>C

AA changes

AAE:	E335A	?
Score:	107

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Epilepsy, familial temporal lobe, 1

pathogenic

Variant DBs

	Not in dbSNP
	Allele 'C' was not found in gnomAD

Protein conservation

Species	Match	AA	Alignment
Human		335	S	L	H	A	W	Y	R	D	T	D	V	E	Y	L	E	I	V	R	T	P	Q	T	L	R
mutated	not conserved	335	S	L	H	A	W	Y	R	D	T	D	V	A	Y	L	E	I	V	R	T	P	Q	T	L
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
35	557	CHAIN		lost
317	364	REPEAT	EAR	lost
331	340	STRAND		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	10.003	1
	9.325	1
(flanking)	3.276	1

?

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

10

Strand

1

Original gDNA sequence snippet

GTACAGGGACACTGATGTGGAATATCTAGAAATAGTCAGAA

Altered gDNA sequence snippet

GTACAGGGACACTGATGTGGCATATCTAGAAATAGTCAGAA

Original cDNA sequence snippet

GTACAGGGACACTGATGTGGAATATCTAGAAATAGTCAGAA

Altered cDNA sequence snippet

GTACAGGGACACTGATGTGGCATATCTAGAAATAGTCAGAA

Wildtype AA sequence

MESERSKRMG NACIPLKRIA YFLCLLSALL LTEGKKPAKP KCPAVCTCTK DNALCENARS
IPRTVPPDVI SLSFVRSGFT EISEGSFLFT PSLQLLSLAN NNLQTLPKDI FKGLDSLTNV
DLRGNSFNCD CKLKWLVEWL GHTNATVEDI YCEGPPEYKK RKINSLSSKD FDCIITEFAK
SQDLPYQSLS IDTFSYLNDE YVVIAQPFTG KCIFLEWDHV EKTFRNYDNI TGTSTVVCKP
IVIETQLYVI VAQLFGGSHI YKRDSFANKF IKIQDIEILK IRKPNDIETF KIENNWYFVV
ADSSKAGFTT IYKWNGNGFY SHQSLHAWYR DTDVEYLEIV RTPQTLRTPH LILSSSSQRP
VIYQWNKATQ LFTNQTDIPN MEDVYAVKHF SVKGDVYICL TRFIGDSKVM KWGGSSFQDI
QRMPSRGSMV FQPLQINNYQ YAILGSDYSF TQVYNWDAEK AKFVKFQELN VQAPRSFTHV
SINKRNFLFA SSFKGNTQIY KHVIVDLSA*

Mutated AA sequence

MESERSKRMG NACIPLKRIA YFLCLLSALL LTEGKKPAKP KCPAVCTCTK DNALCENARS
IPRTVPPDVI SLSFVRSGFT EISEGSFLFT PSLQLLSLAN NNLQTLPKDI FKGLDSLTNV
DLRGNSFNCD CKLKWLVEWL GHTNATVEDI YCEGPPEYKK RKINSLSSKD FDCIITEFAK
SQDLPYQSLS IDTFSYLNDE YVVIAQPFTG KCIFLEWDHV EKTFRNYDNI TGTSTVVCKP
IVIETQLYVI VAQLFGGSHI YKRDSFANKF IKIQDIEILK IRKPNDIETF KIENNWYFVV
ADSSKAGFTT IYKWNGNGFY SHQSLHAWYR DTDVAYLEIV RTPQTLRTPH LILSSSSQRP
VIYQWNKATQ LFTNQTDIPN MEDVYAVKHF SVKGDVYICL TRFIGDSKVM KWGGSSFQDI
QRMPSRGSMV FQPLQINNYQ YAILGSDYSF TQVYNWDAEK AKFVKFQELN VQAPRSFTHV
SINKRNFLFA SSFKGNTQIY KHVIVDLSA*

Position of stopcodon in wt / mu CDS

1530 / 1530

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

510 / 510

Position of stopcodon in wt / mu cDNA

1704 / 1704

Position of start ATG in wt / mu cDNA

175 / 175

Last intron/exon boundary

868

Theoretical NMD boundary in CDS

643

Length of CDS

1530

Coding sequence (CDS) position

1004

cDNA position

1178

gDNA position

39438

Chromosomal position

93797277

Speed

0.11 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:

10:93797277A>C_4_ENST00000637689

Prediction:

DeleteriousPermalink

Summary:

Known disease mutation: ClinVar ID 5430 (pathogenic)

Model: 5utr
Tree vote: 100|0 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr10:93797277A>C (GRCh38)

Gene symbol

Gene constraints

LOEUF: 0.53, LOF (oe): 0.11, misssense (oe): 0.64, synonymous (oe): 0.92 ? (gnomAD)

Ensembl transcript ID

ENST00000637689.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

5'UTR

DNA changes

cDNA.971A>C
g.39438A>C

AA changes

N/A

Frameshift

No

Length of protein

N/A

Pathogenic variant (ClinVar)

Epilepsy, familial temporal lobe, 1

pathogenic

Variant DBs

	Not in dbSNP
	Allele 'C' was not found in gnomAD

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	10.003	1
	9.325	1
(flanking)	3.276	1

?

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

N/A

Chromosome

10

Strand

1

Original gDNA sequence snippet

GTACAGGGACACTGATGTGGAATATCTAGAAATAGTCAGAA

Altered gDNA sequence snippet

GTACAGGGACACTGATGTGGCATATCTAGAAATAGTCAGAA

Original cDNA sequence snippet

GTACAGGGACACTGATGTGGAATATCTAGAAATAGTCAGAA

Altered cDNA sequence snippet

GTACAGGGACACTGATGTGGCATATCTAGAAATAGTCAGAA

Wildtype AA sequence

MKWGGSSFQD IQRMPSRGSM VFQPLQINNY QYAILGSDYS FTQVYNWDAE KAKFVKFQEL
NVQAPRSFTH VSINKRNFLF ASSFKGNTQI YKHVIVDLSA *

Mutated AA sequence

Position of stopcodon in wt / mu CDS

N/A

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

N/A

Position of stopcodon in wt / mu cDNA

N/A

Position of start ATG in wt / mu cDNA

1195 / 1195

Last intron/exon boundary

661

Theoretical NMD boundary in CDS

cannot be calculated, distance between start ATG and last intron/exon boundary is too small

Length of CDS

303

Coding sequence (CDS) position

N/A

cDNA position

971

gDNA position

39438

Chromosomal position

93797277

Speed

0.01 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:

10:93797277A>C_6_ENST00000371413

Prediction:

DeleteriousPermalink

Summary:

Known disease mutation: ClinVar ID 5430 (pathogenic)

Model: without_aae
Tree vote: 197|3 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr10:93797277A>C (GRCh38)

Gene symbol

Gene constraints

LOEUF: 0.54, LOF (oe): 0.30, misssense (oe): 0.66, synonymous (oe): 0.93 ? (gnomAD)

Ensembl transcript ID

ENST00000371413.4

Genbank transcript ID

NM_001308275 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.839-472A>C
g.39438A>C

AA changes

N/A

Frameshift

No

Length of protein

N/A

Pathogenic variant (ClinVar)

Epilepsy, familial temporal lobe, 1

pathogenic

Variant DBs

	Not in dbSNP
	Allele 'C' was not found in gnomAD

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	10.003	1
	9.325	1
(flanking)	3.276	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

10

Strand

1

Original gDNA sequence snippet

GTACAGGGACACTGATGTGGAATATCTAGAAATAGTCAGAA

Altered gDNA sequence snippet

GTACAGGGACACTGATGTGGCATATCTAGAAATAGTCAGAA

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MESERSKRMG NACIPLKRIA YFLCLLSALL LTEGKKPAKP KCPAVCTCTK DNALCENARS
IPRTVPPDVI SLSFVRSGFT EISEGSFLFT PSLQLLLFTS NSFDVISDDA FIGLPHLEYL
FIENNNIKSI SRHTFRGLKS LIHLSLANNN LQTLPKDIFK GLDSLTNVDL RGNSFNCDCK
LKWLVEWLGH TNATVEDIYC EGPPEYKKRK INSLSSKDFD CIITEFAKSQ DLPYQSLSID
TFSYLNDEYV VIAQPFTGKC IFLEWDHVEK TFRNYDNITV LREIHRFTNM S*

Mutated AA sequence

Position of stopcodon in wt / mu CDS

N/A

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

N/A

Position of stopcodon in wt / mu cDNA

N/A

Position of start ATG in wt / mu cDNA

1 / 1

Last intron/exon boundary

838

Theoretical NMD boundary in CDS

787

Length of CDS

876

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

39438

Chromosomal position

93797277

Speed

0.02 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:

10:93797277A>C_5_ENST00000636155

Prediction:

DeleteriousPermalink

Summary:

Known disease mutation: ClinVar ID 5430 (pathogenic)

Model: without_aae
Tree vote: 198|2 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr10:93797277A>C (GRCh38)

Gene symbol

Gene constraints

LOEUF: 0.52, LOF (oe): 0.28, misssense (oe): 0.65, synonymous (oe): 0.91 ? (gnomAD)

Ensembl transcript ID

ENST00000636155.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.838+3927A>C
g.39438A>C

AA changes

N/A

Frameshift

No

Length of protein

N/A

Pathogenic variant (ClinVar)

Epilepsy, familial temporal lobe, 1

pathogenic

Variant DBs

	Not in dbSNP
	Allele 'C' was not found in gnomAD

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	10.003	1
	9.325	1
(flanking)	3.276	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

10

Strand

1

Original gDNA sequence snippet

GTACAGGGACACTGATGTGGAATATCTAGAAATAGTCAGAA

Altered gDNA sequence snippet

GTACAGGGACACTGATGTGGCATATCTAGAAATAGTCAGAA

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MESERSKRMG NACIPLKRIA YFLCLLSALL LTEGKKPAKP KCPAVCTCTK DNALCENARS
IPRTVPPDVI SLSFVRSGFT EISEGSFLFT PSLQLLLFTS NSFDVISDDA FIGLPHLEYL
FIENNNIKSI SRHTFRGLKS LIHLSLANNN LQTLPKDIFK GLDSLTNVDL RGNSFNCDCK
LKWLVEWLGH TNATVEDIYC EGPPEYKKRK INSLSSKDFD CIITEFAKSQ DLPYQSLSID
TFSYLNDEYV VIAQPFTGKC IFLEWDHVEK TFRNYDNITG QSCWCPQ*

Mutated AA sequence

Position of stopcodon in wt / mu CDS

N/A

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

N/A

Position of stopcodon in wt / mu cDNA

N/A

Position of start ATG in wt / mu cDNA

118 / 118

Last intron/exon boundary

955

Theoretical NMD boundary in CDS

787

Length of CDS

864

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

39438

Chromosomal position

93797277

Speed

0.01 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