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: ENST00000647596
Querying Taster for transcript #2: ENST00000493838
Querying Taster for transcript #3: ENST00000398015
MT speed 0.06 s - this script 2.427738 s

Transcript summary:

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Transcript	Gene symbol	Prediction	Tree vote	Model	Splice site change	Variant type	Protein length	Features at a glance
ENST00000647596	EPHB1	Benign	0\|200	without_aae	No	Single base exchange	N/A	Homozygous in gnomAD
ENST00000493838	EPHB1	Benign	0\|200	without_aae	No	Single base exchange	N/A	Homozygous in gnomAD
ENST00000398015(MANE Select)	EPHB1	Benign	0\|200	without_aae	No	Single base exchange	N/A	Homozygous in gnomAD

MutationT@ster 2025

Variant:

3:135214774C>T_1_ENST00000647596

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Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: without_aae
Tree vote: 0|200 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr3:135214774C>T (GRCh38)

Gene symbol

EPHB1

Gene constraints

LOEUF: 0.45, LOF (oe): 0.33, misssense (oe): 0.78, synonymous (oe): 1.02 ? (gnomAD)

Ensembl transcript ID

ENST00000647596.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.2346+13085C>T
g.419515C>T

AA changes

N/A

Frameshift

No

Length of protein

N/A

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs4309752
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	7128	31818	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.334	0.005
	0.341	0.003
(flanking)	0.232	0.002

?

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

3

Strand

1

Original gDNA sequence snippet

GCCCTTCCTTTCACAAAATTCGGCCTTCATTCATGATATTG

Altered gDNA sequence snippet

GCCCTTCCTTTCACAAAATTTGGCCTTCATTCATGATATTG

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MALDYLLLLL LASAVAAMEE TLMDTRTATA ELGWTANPAS GWEEVSGYDE NLNTIRTYQV
CNVFEPNQNN WLLTTFINRR GAHRIYTEMR FTVRDCSSLP NVPGSCKETF NLYYYETDSV
IATKKSAFWS EAPYLKVDTI AADESFSQVD FGGRLMKVNT EVRSFGPLTR NGFYLAFQDY
GACMSLLSVR VFFKKCPSIV QNFAVFPETM TGAESTSLVI ARGTCIPNAE EVDVPIKLYC
NGDGEWMVPI GRCTCKPGYE PENSVACKAC PAGTFKASQE AEGCSHCPSN SRSPAEASPI
CTCRTGYYRA DFDPPEVACT SVPSGPRNVI SIVNETSIIL EWHPPRETGG RDDVTYNIIC
KKCRADRRSC SRCDDNVEFV PRQLGLTECR VSISSLWAHT PYTFDIQAIN GVSSKSPFPP
QHVSVNITTN QAAPSTVPIM HQVSATMRSI TLSWPQPEQP NGIILDYEIR YYEKEHNEFN
SSMARSQTNT ARIDGLRPGM VYVVQVRART VAGYGKFSGK MCFQTLTDDD YKSELREQLP
LIAGSAAAGV VFVVSLVAIS IVCSRKRAYS KEAVYSDKLQ HYSTGRGSPG MKIYIDPFTY
EDPNEAVREF AKEIDVSFVK IEEVIGAGEF GEVYKGRLKL PGKREIYVAI KTLKAGYSEK
QRRDFLSEAS IMGQFDHPNI IRLEGVVTKS RPVMIITEFM ENGALDSFLR QNDGQFTVIQ
LVGMLRGIAA GMKYLAEMNY VHRDLAARNI LVNSNLVCKV SDFGLSRYLQ DDTSDPTYTS
SLGGKIPVRW TAPEAIAYRK FTSASDVWSY GIVMWEVMSF GERPYWDMSN QDVINAIEQD
YRLPPPMDCP AALHQLMLDC WQKDRNSRPR FAEIVNTLDK MIRNPASLKT VATITAVPSQ
PLLDRSIPDF TAFTTVDDWL SAIKMVQYRD SFLTAGFTSL QLVTQMTSEH HLGRPSEEDP
EQHSFYEGPD KSVTNGNGMR TLVSWGRRGG KRTRVKGDQR LTTVECTGET GFSAEECISI
SEESTGPVAS RQSPFLSDRS MFEMPWETKY IIIKI*

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

341 / 341

Last intron/exon boundary

3186

Theoretical NMD boundary in CDS

2795

Length of CDS

3168

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

419515

Chromosomal position

135214774

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

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MutationT@ster 2025

Variant:

3:135214774C>T_2_ENST00000493838

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Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: without_aae
Tree vote: 0|200 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr3:135214774C>T (GRCh38)

Gene symbol

EPHB1

Gene constraints

LOEUF: 0.57, LOF (oe): 0.40, misssense (oe): 0.79, synonymous (oe): 1.02 ? (gnomAD)

Ensembl transcript ID

ENST00000493838.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.1029+13085C>T
g.419515C>T

AA changes

N/A

Frameshift

No

Length of protein

N/A

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs4309752
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	7128	31818	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.334	0.005
	0.341	0.003
(flanking)	0.232	0.002

?

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

3

Strand

1

Original gDNA sequence snippet

GCCCTTCCTTTCACAAAATTCGGCCTTCATTCATGATATTG

Altered gDNA sequence snippet

GCCCTTCCTTTCACAAAATTTGGCCTTCATTCATGATATTG

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MHQVSATMRS ITLSWPQPEQ PNGIILDYEI RYYEKEHNEF NSSMARSQTN TARIDGLRPG
MVYVVQVRAR TVAGYGKFSG KMCFQTLTDD DYKSELREQL PLIAGSAAAG VVFVVSLVAI
SIVCSRKRAY SKEAVYSDKL QHYSTGRGSP GMKIYIDPFT YEDPNEAVRE FAKEIDVSFV
KIEEVIGAGE FGEVYKGRLK LPGKREIYVA IKTLKAGYSE KQRRDFLSEA SIMGQFDHPN
IIRLEGVVTK SRPVMIITEF MENGALDSFL RQNDGQFTVI QLVGMLRGIA AGMKYLAEMN
YVHRDLAARN ILVNSNLVCK VSDFGLSRYL QDDTSDPTYT SSLGGKIPVR WTAPEAIAYR
KFTSASDVWS YGIVMWEVMS FGERPYWDMS NQDVINAIEQ DYRLPPPMDC PAALHQLMLD
CWQKDRNSRP RFAEIVNTLD KMIRNPASLK TVATITAVPS QPLLDRSIPD FTAFTTVDDW
LSAIKMVQYR DSFLTAGFTS LQLVTQMTSE DLLRIGITLA GHQKKILNSI HSMRVQISQS
PTAMA*

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

899 / 899

Last intron/exon boundary

2427

Theoretical NMD boundary in CDS

1478

Length of CDS

1638

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

419515

Chromosomal position

135214774

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

Back to summary table

MutationT@ster 2025

Variant:

3:135214774C>T_3_ENST00000398015

Back to summary table

Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: without_aae
Tree vote: 0|200 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr3:135214774C>T (GRCh38)

Gene symbol

EPHB1

Gene constraints

LOEUF: 0.44, LOF (oe): 0.33, misssense (oe): 0.77, synonymous (oe): 1.02 ? (gnomAD)

Ensembl transcript ID

ENST00000398015.8

Genbank transcript ID

NM_004441 (exact from MANE)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.2346+13085C>T
g.419515C>T

AA changes

N/A

Frameshift

No

Length of protein

N/A

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs4309752
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	7128	31818	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.334	0.005
	0.341	0.003
(flanking)	0.232	0.002

?

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

3

Strand

1

Original gDNA sequence snippet

GCCCTTCCTTTCACAAAATTCGGCCTTCATTCATGATATTG

Altered gDNA sequence snippet

GCCCTTCCTTTCACAAAATTTGGCCTTCATTCATGATATTG

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MALDYLLLLL LASAVAAMEE TLMDTRTATA ELGWTANPAS GWEEVSGYDE NLNTIRTYQV
CNVFEPNQNN WLLTTFINRR GAHRIYTEMR FTVRDCSSLP NVPGSCKETF NLYYYETDSV
IATKKSAFWS EAPYLKVDTI AADESFSQVD FGGRLMKVNT EVRSFGPLTR NGFYLAFQDY
GACMSLLSVR VFFKKCPSIV QNFAVFPETM TGAESTSLVI ARGTCIPNAE EVDVPIKLYC
NGDGEWMVPI GRCTCKPGYE PENSVACKAC PAGTFKASQE AEGCSHCPSN SRSPAEASPI
CTCRTGYYRA DFDPPEVACT SVPSGPRNVI SIVNETSIIL EWHPPRETGG RDDVTYNIIC
KKCRADRRSC SRCDDNVEFV PRQLGLTECR VSISSLWAHT PYTFDIQAIN GVSSKSPFPP
QHVSVNITTN QAAPSTVPIM HQVSATMRSI TLSWPQPEQP NGIILDYEIR YYEKEHNEFN
SSMARSQTNT ARIDGLRPGM VYVVQVRART VAGYGKFSGK MCFQTLTDDD YKSELREQLP
LIAGSAAAGV VFVVSLVAIS IVCSRKRAYS KEAVYSDKLQ HYSTGRGSPG MKIYIDPFTY
EDPNEAVREF AKEIDVSFVK IEEVIGAGEF GEVYKGRLKL PGKREIYVAI KTLKAGYSEK
QRRDFLSEAS IMGQFDHPNI IRLEGVVTKS RPVMIITEFM ENGALDSFLR QNDGQFTVIQ
LVGMLRGIAA GMKYLAEMNY VHRDLAARNI LVNSNLVCKV SDFGLSRYLQ DDTSDPTYTS
SLGGKIPVRW TAPEAIAYRK FTSASDVWSY GIVMWEVMSF GERPYWDMSN QDVINAIEQD
YRLPPPMDCP AALHQLMLDC WQKDRNSRPR FAEIVNTLDK MIRNPASLKT VATITAVPSQ
PLLDRSIPDF TAFTTVDDWL SAIKMVQYRD SFLTAGFTSL QLVTQMTSED LLRIGITLAG
HQKKILNSIH SMRVQISQSP TAMA*

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

373 / 373

Last intron/exon boundary

3218

Theoretical NMD boundary in CDS

2795

Length of CDS

2955

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

419515

Chromosomal position

135214774

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

Back to summary table