MutationT@ster 2025

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Input seems to be ok - now mapping the variant to the different transcripts...
Querying Taster for transcript #1: ENST00000371418
Querying Taster for transcript #2: ENST00000629035
Querying Taster for transcript #3: ENST00000630047
Querying Taster for transcript #4: ENST00000637689
Querying Taster for transcript #5: ENST00000636155
Querying Taster for transcript #6: ENST00000371413
MT speed 0.46 s - this script 2.912748 s

Transcript summary:

Permalink

Transcript	Gene symbol	Prediction	Tree vote	Model	Splice site change	Amino acid changes	Variant type	Protein length	Features at a glance
ENST00000629035	LGI1	Deleterious	10\|0	complex_aae	No	A229Vfs*32	Deletion	Strongly truncated protein, might cause NMD (-274 AA / more than 10% missing)	Amino acid sequence changed Frameshift Truncated protein (might cause NMD)
ENST00000636155	LGI1	Deleterious	10\|0	complex_aae	No	original stopcodon lost	Deletion	Prolonged protein (+15 AA)	Amino acid sequence changed Prolonged protein
ENST00000630047	LGI1	Deleterious	10\|0	complex_aae	No	A205Vfs*32	Deletion	Strongly truncated protein, might cause NMD (-274 AA / more than 10% missing)	Amino acid sequence changed Frameshift Protein features (might be) affected Truncated protein (might cause NMD)
ENST00000371418(MANE Select)	LGI1	Deleterious	10\|0	complex_aae	No	A253Vfs*32	Deletion	Strongly truncated protein, might cause NMD (-274 AA / more than 10% missing)	Amino acid sequence changed Frameshift Protein features (might be) affected Truncated protein (might cause NMD)
ENST00000371413	LGI1	Deleterious	10\|0	complex_aae	No	A253Vfs*29	Deletion	Slightly truncated protein, might cause NMD (-11 AA / less than 10% missing)	Amino acid sequence changed Frameshift Protein features (might be) affected Truncated protein (might cause NMD)
ENST00000637689	LGI1	Deleterious	99\|1	5utr	No		Deletion	N/A

MutationT@ster 2025

Variant:

10:93793269GC>G_2_ENST00000629035

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Frameshift
Truncated protein (might cause NMD)

Model: complex_aae
Tree vote: 10|0 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr10:93793270delC (GRCh38)

Gene symbol

LGI1

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

Deletion

Gene region

CDS

DNA changes

c.686delC
g.35431delC

AA changes

A229Vfs*32

Frameshift

Yes

Length of protein

Strongly truncated protein, might cause NMD (-274 AA / more than 10% missing)

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

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

Protein conservation

Species	Match	AA	Alignment
Human		229	F	S	Y	L	N	D	E	Y	V	V	I	A	Q	P	F	T	G	K	C	I	F	L	E	W
mutated	no alignment	n/a
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
	6.171	1
(flanking)	0.608	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

TGATGAGTATGTAGTCATCGCTCAGCCTTTTACTGGAAAAT

Altered gDNA sequence snippet

TGATGAGTATGTAGTCATCGTCAGCCTTTTACTGGAAAAT

Original cDNA sequence snippet

TGATGAGTATGTAGTCATCGCTCAGCCTTTTACTGGAAAAT

Altered cDNA sequence snippet

TGATGAGTATGTAGTCATCGTCAGCCTTTTACTGGAAAAT

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 LNDEYVVIVS LLLENAFSLN
GTMWKRPSGI MTTLQAHPL*

Position of stopcodon in wt / mu CDS

1602 / 780

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

534 / 260

Position of stopcodon in wt / mu cDNA

1896 / 1074

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

685 / 687

cDNA position

979 / 981

gDNA position

35430 / 35432

Chromosomal position

93793269 / 93793271

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

MutationT@ster 2025

Variant:

10:93793269GC>G_5_ENST00000636155

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Prolonged protein

Model: complex_aae
Tree vote: 10|0 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr10:93793270delC (GRCh38)

Gene symbol

LGI1

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

Deletion

Gene region

CDS

DNA changes

c.758delC
g.35431delC

AA changes

original stopcodon lost, results in prolonged protein

AAE:	A253V	Q254S	P255L	F256L	T257L	G258E	K259N	C260A	I261F	F262S	E264N	W265G	D266T	H267M	V268W	E269K	K270R	T271P	F272S	R273G	N274I	Y275M	D276T	N277T	I278L	T279Q	G280V	Q281N	S282P	C283V	W284G	C285V	P286H	Q287N	*288S	-289S	-289L	-289S	-289G	-289A	-289V	-289G	-289I	-289V	-289V	-289T	-289A	-289C	-289V	-289*	?
Score:	64	68	98	22	92	98	94	195	21	155	42	184	85	87	88	56	26	38	155	125	149	36	85	65	5	42	109	46	74	192	184	192	77	46	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-

Frameshift

No

Length of protein

Prolonged protein (+15 AA)

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

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

Protein conservation

Species	Match	AA	Alignment
Human		253	F	S	Y	L	N	D	E	Y	V	V	I	A	Q	P	F	T	G	K	C	I	F	L	E	W	D	H	V	E	K	T	F	R	N	Y	D	N	I	T	G	Q	S	C	W	C	P	Q	*
mutated	partly conserved	253	F	S	Y	L	N	D	E	Y	V	V	I	V	S	L	L	L	E	N	A	F	S	L	N	G	T	M	W	K	R	P	S	G	I	M	T	T	L	Q	V	N	P	V	G	V	H	N	s	s	l	s	g	a	v	g	i	v	v	t	a
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
	6.171	1
(flanking)	0.608	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

TGATGAGTATGTAGTCATCGCTCAGCCTTTTACTGGAAAAT

Altered gDNA sequence snippet

TGATGAGTATGTAGTCATCGTCAGCCTTTTACTGGAAAAT

Original cDNA sequence snippet

TGATGAGTATGTAGTCATCGCTCAGCCTTTTACTGGAAAAT

Altered cDNA sequence snippet

TGATGAGTATGTAGTCATCGTCAGCCTTTTACTGGAAAAT

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

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 VIVSLLLENA FSLNGTMWKR PSGIMTTLQV NPVGVHNSSL SGAVGIVVTA
CV*

Position of stopcodon in wt / mu CDS

864 / 909

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

288 / 303

Position of stopcodon in wt / mu cDNA

981 / 1026

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

757 / 759

cDNA position

874 / 876

gDNA position

35430 / 35432

Chromosomal position

93793269 / 93793271

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

MutationT@ster 2025

Variant:

10:93793269GC>G_3_ENST00000630047

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Frameshift
Protein features (might be) affected
Truncated protein (might cause NMD)

Model: complex_aae
Tree vote: 10|0 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr10:93793270delC (GRCh38)

Gene symbol

LGI1

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

Deletion

Gene region

CDS

DNA changes

c.614delC
g.35431delC

AA changes

A205Vfs*32

Frameshift

Yes

Length of protein

Strongly truncated protein, might cause NMD (-274 AA / more than 10% missing)

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

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

Protein conservation

Species	Match	AA	Alignment
Human		205	F	S	Y	L	N	D	E	Y	V	V	I	A	Q	P	F	T	G	K	C	I	F	L	E	W
mutated	no alignment	n/a
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
173	223	DOMAIN	LRRCT	lost
204	206	HELIX		lost
211	213	HELIX		lost
216	218	HELIX		lost
225	234	STRAND		lost
225	267	REPEAT	EAR	lost
239	244	STRAND		lost
247	253	STRAND		lost
255	257	TURN		lost
259	266	STRAND		lost
267	270	TURN		lost
271	279	STRAND		lost
271	313	REPEAT	EAR	lost
277	277	CARBOHYD	N-linked (GlcNAc...) asparagine	lost
283	291	STRAND		lost
294	304	STRAND		lost
307	312	STRAND		lost
313	316	TURN		lost
317	323	STRAND		lost
317	364	REPEAT	EAR	lost
326	328	TURN		lost
331	340	STRAND		lost
343	350	STRAND		lost
352	355	STRAND		lost
357	362	STRAND		lost
366	415	REPEAT	EAR	lost
367	374	STRAND		lost
379	387	STRAND		lost
396	403	STRAND		lost
409	414	STRAND		lost
415	418	TURN		lost
419	425	STRAND		lost
419	462	REPEAT	EAR	lost
422	422	CARBOHYD	N-linked (GlcNAc...) asparagine	lost
434	440	STRAND		lost
443	449	STRAND		lost
451	461	STRAND		lost
464	475	STRAND		lost
464	506	REPEAT	EAR	lost
479	484	STRAND		lost
487	492	STRAND		lost
495	497	STRAND		lost
499	505	STRAND		lost
506	509	TURN		lost
510	517	STRAND		lost
510	552	REPEAT	EAR	lost
520	530	STRAND		lost
533	543	STRAND		lost
545	551	STRAND		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	10.003	1
	6.171	1
(flanking)	0.608	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

TGATGAGTATGTAGTCATCGCTCAGCCTTTTACTGGAAAAT

Altered gDNA sequence snippet

TGATGAGTATGTAGTCATCGTCAGCCTTTTACTGGAAAAT

Original cDNA sequence snippet

TGATGAGTATGTAGTCATCGCTCAGCCTTTTACTGGAAAAT

Altered cDNA sequence snippet

TGATGAGTATGTAGTCATCGTCAGCCTTTTACTGGAAAAT

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 YVVIVSLLLE NAFSLNGTMW KRPSGIMTTL QAHPL*

Position of stopcodon in wt / mu CDS

1530 / 708

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

510 / 236

Position of stopcodon in wt / mu cDNA

1704 / 882

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

613 / 615

cDNA position

787 / 789

gDNA position

35430 / 35432

Chromosomal position

93793269 / 93793271

Speed

0.10 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

Back to summary table

MutationT@ster 2025

Variant:

10:93793269GC>G_1_ENST00000371418

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Frameshift
Protein features (might be) affected
Truncated protein (might cause NMD)

Model: complex_aae
Tree vote: 10|0 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr10:93793270delC (GRCh38)

Gene symbol

LGI1

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

Deletion

Gene region

CDS

DNA changes

c.758delC
g.35431delC

AA changes

A253Vfs*32

Frameshift

Yes

Length of protein

Strongly truncated protein, might cause NMD (-274 AA / more than 10% missing)

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

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

Protein conservation

Species	Match	AA	Alignment
Human		253	F	S	Y	L	N	D	E	Y	V	V	I	A	Q	P	F	T	G	K	C	I	F	L	E	W	D	H	V	E	K	T	F	R	N	Y	D	N	I	T	G	T	S	T	V	V	C	K	P	I	V	I	E	T	Q	L	Y	V	I	V	A	Q	L	F	G	G	S	H	I	Y	K	R	D	S	F	A	N	K	F	I	K	I	Q	D	I	E	I	L	K	I	R	K	P	N	D	I	E	T	F	K	I	E	N	N	W	Y	F	V	V	A	D	S	S	K	A	G	F	T	T	I	Y	K	W	N	G	N	G	F	Y	S	H	Q	S	L	H	A	W	Y	R	D	T
mutated	no alignment	n/a
Ptroglodytes	all identical	253	F	S	Y	L	N	D	E	Y	V	V	I	A	Q	P	F	T	G	K	C	I	F	L	E	W	D	H	V	E	K	T	F	R	N	Y	D	N	I	T	G	T	S	T	V	V	C	K	P	I	V	I	E	T	Q	L	Y	V	I	V	A	Q	L	F	G	G	S	H	I	Y	K	R	D	S	F	A	N	K	F	I	K	I	Q	D	I	E	I	L	K	I	R	K	P	N	D	I	E	T	F	K	I	E	N	N	W	Y	F	V	V	A	D	S	S	K	A	G	F	T	T	I	Y
Mmulatta	all identical	253	F	S	Y	L	N	D	E	Y	V	V	I	A	Q	P	F	T	G	K	C	I	F	L	E	W	D	H	V	E	K	T	F	R	N	Y	D	N	I	T	G	T	S	T	V	V	C	K	P	I	V	I	E	T	Q	L	Y	V	I	V	A	Q	L	F	G	G	S	H	I	Y	K	R	D	S	F	A	N	K	F	I	K	I	Q	D	I	E	I	L	K	I	R	K	P	N	D	I	E	T	F	K	I	E	N	N	W	Y	F	V	V	A	D	S	S	K	A	G	F	T	T	I	Y
Fcatus	all identical	253	F	S	Y	M	N	D	E	Y	V	V	I	A	Q	P	F	T	G	K	C	I	F	L	E	W	D	H	V	E	K	T	F	R	N	Y	D	N	I	T	G	T	S	T	V	V	C	K	P	I	V	I	E	T	Q	L	Y	V	I	V	A	Q	L	F	G	G	S	H	I	Y	K	R	D	S	F	A	N	K	F	I	K	I	Q	D	I	E	I	L	K	I	R	K	P	N	D	I	E	T	F	K	I	E	N	N	W	Y	F	V	V	A	D	S	S	K	A	G	F	T	T	I	Y
Mmusculus	partly conserved	253	F	S	Y	L	N	D	E	Y	V	V	I	A	Q	P	F	T	G	K	C	I	F	L	E	W	D	H	V	E	K	T	F	R	N	Y	D	N	I	T	G	T	S	T	V	V	C	K	P	I	V	I	D	T	Q	L	Y	V	I	V	A	Q	L	F	G	G	S	H	I	Y	K	R	D	G	F	A	N	K	F	I	K	I	Q	D	I	E	V	L	K	I	R	K	P	N	D	I	E	T	F	K	I	E	D	N	W	Y	F	V	V	A	D	S	S	K	A	G	F	T	T	I	Y
Ggallus	partly conserved	245								H	V	V	I	A	Q	P	F	T	G	K	C	I	F	L	E	W	D	H	V	E	V	M	F	R	N	Y	D	N	I	T	G	T	S	T	V	V	C	K	P	I	V	I	E	S	Q	L	Y	V	I	V	A	Q	L	F	G	G	S	H	I	Y	K	R	D	I	F	A	N	K	F	I	K	I	Q	D	I	E	I	L	K	I	R	K	P	N	D	I	E	T	F	R	I	A	E	D	W	Y	F	V	V	A	D	S	S	K	A	G	F	T	T	V	Y	K	W	N	G	N	G	F	Y
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	partly conserved	248					N	D	E	Y	V	V	I	A	Q	P	F	T	G	K	C	I	F	L	E	W	D	H	V	E	M	S	F	R	N	Y	D	N	I	T	G	T	S	T	V	V	C	K	P	I	V	I	E	K	Q	L	Y	V	I	V	A	Q	L	F	G	G	S	H	I	Y	K	R	D	I	F	A	N	K	F	I	K	I	Q	D	I	E	I	L	K	I	R	K	P	N	D	I	E	T	F	R	I	D	E	N	W	Y	F	V	V	A	D	S	S	K	A	G	F	T	T	I	Y	K	W	N	G	N

Protein features

Start (aa)	End (aa)	Feature	Details
35	557	CHAIN		lost
225	267	REPEAT	EAR	lost
247	253	STRAND		lost
255	257	TURN		lost
259	266	STRAND		lost
267	270	TURN		lost
271	279	STRAND		lost
271	313	REPEAT	EAR	lost
277	277	CARBOHYD	N-linked (GlcNAc...) asparagine	lost
283	291	STRAND		lost
294	304	STRAND		lost
307	312	STRAND		lost
313	316	TURN		lost
317	323	STRAND		lost
317	364	REPEAT	EAR	lost
326	328	TURN		lost
331	340	STRAND		lost
343	350	STRAND		lost
352	355	STRAND		lost
357	362	STRAND		lost
366	415	REPEAT	EAR	lost
367	374	STRAND		lost
379	387	STRAND		lost
396	403	STRAND		lost
409	414	STRAND		lost
415	418	TURN		lost
419	425	STRAND		lost
419	462	REPEAT	EAR	lost
422	422	CARBOHYD	N-linked (GlcNAc...) asparagine	lost
434	440	STRAND		lost
443	449	STRAND		lost
451	461	STRAND		lost
464	475	STRAND		lost
464	506	REPEAT	EAR	lost
479	484	STRAND		lost
487	492	STRAND		lost
495	497	STRAND		lost
499	505	STRAND		lost
506	509	TURN		lost
510	517	STRAND		lost
510	552	REPEAT	EAR	lost
520	530	STRAND		lost
533	543	STRAND		lost
545	551	STRAND		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	10.003	1
	6.171	1
(flanking)	0.608	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

TGATGAGTATGTAGTCATCGCTCAGCCTTTTACTGGAAAAT

Altered gDNA sequence snippet

TGATGAGTATGTAGTCATCGTCAGCCTTTTACTGGAAAAT

Original cDNA sequence snippet

TGATGAGTATGTAGTCATCGCTCAGCCTTTTACTGGAAAAT

Altered cDNA sequence snippet

TGATGAGTATGTAGTCATCGTCAGCCTTTTACTGGAAAAT

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 VIVSLLLENA FSLNGTMWKR PSGIMTTLQA HPL*

Position of stopcodon in wt / mu CDS

1674 / 852

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

558 / 284

Position of stopcodon in wt / mu cDNA

1883 / 1061

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

757 / 759

cDNA position

966 / 968

gDNA position

35430 / 35432

Chromosomal position

93793269 / 93793271

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

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MutationT@ster 2025

Variant:

10:93793269GC>G_6_ENST00000371413

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Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Frameshift
Protein features (might be) affected
Truncated protein (might cause NMD)

Model: complex_aae
Tree vote: 10|0 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr10:93793270delC (GRCh38)

Gene symbol

LGI1

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

LGI1_HUMAN | AlphaMissense: transcript, gene

Variant type

Deletion

Gene region

CDS

DNA changes

c.758delC
g.35431delC

AA changes

A253Vfs*29

Frameshift

Yes

Length of protein

Slightly truncated protein, might cause NMD (-11 AA / less than 10% missing)

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

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

Protein conservation

Species	Match	AA	Alignment
Human		253	F	S	Y	L	N	D	E	Y	V	V	I	A	Q	P	F	T	G	K	C	I	F	L	E	W
mutated	no alignment	n/a
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
225	267	REPEAT	EAR	lost
247	253	STRAND		lost
255	257	TURN		lost
259	266	STRAND		lost
267	270	TURN		lost
271	279	STRAND		lost
271	313	REPEAT	EAR	lost
277	277	CARBOHYD	N-linked (GlcNAc...) asparagine	lost
283	291	STRAND		lost
294	304	STRAND		lost
307	312	STRAND		lost
313	316	TURN		lost
317	323	STRAND		lost
317	364	REPEAT	EAR	lost
326	328	TURN		lost
331	340	STRAND		lost
343	350	STRAND		lost
352	355	STRAND		lost
357	362	STRAND		lost
366	415	REPEAT	EAR	lost
367	374	STRAND		lost
379	387	STRAND		lost
396	403	STRAND		lost
409	414	STRAND		lost
415	418	TURN		lost
419	425	STRAND		lost
419	462	REPEAT	EAR	lost
422	422	CARBOHYD	N-linked (GlcNAc...) asparagine	lost
434	440	STRAND		lost
443	449	STRAND		lost
451	461	STRAND		lost
464	475	STRAND		lost
464	506	REPEAT	EAR	lost
479	484	STRAND		lost
487	492	STRAND		lost
495	497	STRAND		lost
499	505	STRAND		lost
506	509	TURN		lost
510	517	STRAND		lost
510	552	REPEAT	EAR	lost
520	530	STRAND		lost
533	543	STRAND		lost
545	551	STRAND		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	10.003	1
	6.171	1
(flanking)	0.608	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

TGATGAGTATGTAGTCATCGCTCAGCCTTTTACTGGAAAAT

Altered gDNA sequence snippet

TGATGAGTATGTAGTCATCGTCAGCCTTTTACTGGAAAAT

Original cDNA sequence snippet

TGATGAGTATGTAGTCATCGCTCAGCCTTTTACTGGAAAAT

Altered cDNA sequence snippet

TGATGAGTATGTAGTCATCGTCAGCCTTTTACTGGAAAAT

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

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 VIVSLLLENA FSLNGTMWKR PSGIMTTLQF *

Position of stopcodon in wt / mu CDS

876 / 843

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

292 / 281

Position of stopcodon in wt / mu cDNA

876 / 843

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

757 / 759

cDNA position

757 / 759

gDNA position

35430 / 35432

Chromosomal position

93793269 / 93793271

Speed

0.04 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

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MutationT@ster 2025

Variant:

10:93793269GC>G_4_ENST00000637689

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Prediction:

DeleteriousPermalink

Summary:

Model: 5utr
Tree vote: 99|1 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr10:93793270delC (GRCh38)

Gene symbol

LGI1

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

Deletion

Gene region

5'UTR

DNA changes

cDNA.581delC
g.35431delC

AA changes

N/A

Frameshift

No

Length of protein

N/A

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

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

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	10.003	1
	6.171	1
(flanking)	0.608	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

TGATGAGTATGTAGTCATCGCTCAGCCTTTTACTGGAAAAT

Altered gDNA sequence snippet

TGATGAGTATGTAGTCATCGTCAGCCTTTTACTGGAAAAT

Original cDNA sequence snippet

TGATGAGTATGTAGTCATCGCTCAGCCTTTTACTGGAAAAT

Altered cDNA sequence snippet

TGATGAGTATGTAGTCATCGTCAGCCTTTTACTGGAAAAT

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

580 / 582

gDNA position

35430 / 35432

Chromosomal position

93793269 / 93793271

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

Back to summary table