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: ENST00000338635
Querying Taster for transcript #2: ENST00000396027
Querying Taster for transcript #3: ENST00000511817
Querying Taster for transcript #4: ENST00000282268
MT speed 0.08 s - this script 2.452363 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
ENST00000338635	XRCC4	Benign	0\|200	without_aae	No	Single base exchange	N/A	Homozygous in gnomAD
ENST00000396027(MANE Select)	XRCC4	Benign	0\|200	without_aae	No	Single base exchange	N/A	Homozygous in gnomAD
ENST00000511817	XRCC4	Benign	0\|200	without_aae	No	Single base exchange	N/A	Homozygous in gnomAD
ENST00000282268	XRCC4	Benign	0\|200	without_aae	No	Single base exchange	N/A	Homozygous in gnomAD

MutationT@ster 2025

Variant:

5:83209037C>T_1_ENST00000338635

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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

Chr5:83209037C>T (GRCh38)

Gene symbol

XRCC4

Gene constraints

LOEUF: 1.06, LOF (oe): 0.77, misssense (oe): 0.90, synonymous (oe): 0.92 ? (gnomAD)

Ensembl transcript ID

ENST00000338635.10

Genbank transcript ID

NM_022406 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.745+4116C>T
g.131540C>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	rs10514249
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	25468	>32000	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.734	0.001
	0.299	0.001
(flanking)	-0.168	0.001

?

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

5

Strand

1

Original gDNA sequence snippet

TGGTATTAAGTACTTGTGGCCTTAAAGATTTCCTGCTTAGT

Altered gDNA sequence snippet

TGGTATTAAGTACTTGTGGCTTTAAAGATTTCCTGCTTAGT

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MERKISRIHL VSEPSITHFL QVSWEKTLES GFVITLTDGH SAWTGTVSES EISQEADDMA
MEKGKYVGEL RKALLSGAGP ADVYTFNFSK ESCYFFFEKN LKDVSFRLGS FNLEKVENPA
EVIRELICYC LDTIAENQAK NEHLQKENER LLRDWNDVQG RFEKCVSAKE ALETDLYKRF
ILVLNEKKTK IRSLHNKLLN AAQEREKDIK QEGETAICSE MTADRDPVYD ESTDEESENQ
TDLSGLASAA VSKDDSIISS LDVTDIAPSR KRRQRMQRNL GTEPKMAPQE NQLQEKENSR
PDSSLPETSK KEHISAENMS LETLRNSSPE DLFDEI*

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

100 / 100

Last intron/exon boundary

992

Theoretical NMD boundary in CDS

842

Length of CDS

1011

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

131540

Chromosomal position

83209037

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:

5:83209037C>T_2_ENST00000396027

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

Chr5:83209037C>T (GRCh38)

Gene symbol

XRCC4

Gene constraints

LOEUF: 1.03, LOF (oe): 0.75, misssense (oe): 0.89, synonymous (oe): 0.92 ? (gnomAD)

Ensembl transcript ID

ENST00000396027.9

Genbank transcript ID

NM_003401 (exact from MANE), NM_001318013 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.745+4116C>T
g.131540C>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	rs10514249
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	25468	>32000	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.734	0.001
	0.299	0.001
(flanking)	-0.168	0.001

?

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

5

Strand

1

Original gDNA sequence snippet

TGGTATTAAGTACTTGTGGCCTTAAAGATTTCCTGCTTAGT

Altered gDNA sequence snippet

TGGTATTAAGTACTTGTGGCTTTAAAGATTTCCTGCTTAGT

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MERKISRIHL VSEPSITHFL QVSWEKTLES GFVITLTDGH SAWTGTVSES EISQEADDMA
MEKGKYVGEL RKALLSGAGP ADVYTFNFSK ESCYFFFEKN LKDVSFRLGS FNLEKVENPA
EVIRELICYC LDTIAENQAK NEHLQKENER LLRDWNDVQG RFEKCVSAKE ALETDLYKRF
ILVLNEKKTK IRSLHNKLLN AAQEREKDIK QEGETAICSE MTADRDPVYD ESTDEESENQ
TDLSGLASAA VSKDDSIISS LDVTDIAPSR KRRQRMQRNL GTEPKMAPQE NQLQEKEKPD
SSLPETSKKE HISAENMSLE TLRNSSPEDL FDEI*

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

80 / 80

Last intron/exon boundary

972

Theoretical NMD boundary in CDS

842

Length of CDS

1005

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

131540

Chromosomal position

83209037

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:

5:83209037C>T_3_ENST00000511817

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

Chr5:83209037C>T (GRCh38)

Gene symbol

XRCC4

Gene constraints

LOEUF: 1.06, LOF (oe): 0.77, misssense (oe): 0.90, synonymous (oe): 0.92 ? (gnomAD)

Ensembl transcript ID

ENST00000511817.1

Genbank transcript ID

NM_001318012 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.745+4116C>T
g.131540C>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	rs10514249
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	25468	>32000	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.734	0.001
	0.299	0.001
(flanking)	-0.168	0.001

?

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

5

Strand

1

Original gDNA sequence snippet

TGGTATTAAGTACTTGTGGCCTTAAAGATTTCCTGCTTAGT

Altered gDNA sequence snippet

TGGTATTAAGTACTTGTGGCTTTAAAGATTTCCTGCTTAGT

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MERKISRIHL VSEPSITHFL QVSWEKTLES GFVITLTDGH SAWTGTVSES EISQEADDMA
MEKGKYVGEL RKALLSGAGP ADVYTFNFSK ESCYFFFEKN LKDVSFRLGS FNLEKVENPA
EVIRELICYC LDTIAENQAK NEHLQKENER LLRDWNDVQG RFEKCVSAKE ALETDLYKRF
ILVLNEKKTK IRSLHNKLLN AAQEREKDIK QEGETAICSE MTADRDPVYD ESTDEESENQ
TDLSGLASAA VSKDDSIISS LDVTDIAPSR KRRQRMQRNL GTEPKMAPQE NQLQEKENSR
PDSSLPETSK KEHISAENMS LETLRNSSPE DLFDEI*

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

81 / 81

Last intron/exon boundary

973

Theoretical NMD boundary in CDS

842

Length of CDS

1011

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

131540

Chromosomal position

83209037

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:

5:83209037C>T_4_ENST00000282268

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

Chr5:83209037C>T (GRCh38)

Gene symbol

XRCC4

Gene constraints

LOEUF: 1.03, LOF (oe): 0.75, misssense (oe): 0.89, synonymous (oe): 0.92 ? (gnomAD)

Ensembl transcript ID

ENST00000282268.7

Genbank transcript ID

NM_022550 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.745+4116C>T
g.131540C>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	rs10514249
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	25468	>32000	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.734	0.001
	0.299	0.001
(flanking)	-0.168	0.001

?

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

5

Strand

1

Original gDNA sequence snippet

TGGTATTAAGTACTTGTGGCCTTAAAGATTTCCTGCTTAGT

Altered gDNA sequence snippet

TGGTATTAAGTACTTGTGGCTTTAAAGATTTCCTGCTTAGT

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MERKISRIHL VSEPSITHFL QVSWEKTLES GFVITLTDGH SAWTGTVSES EISQEADDMA
MEKGKYVGEL RKALLSGAGP ADVYTFNFSK ESCYFFFEKN LKDVSFRLGS FNLEKVENPA
EVIRELICYC LDTIAENQAK NEHLQKENER LLRDWNDVQG RFEKCVSAKE ALETDLYKRF
ILVLNEKKTK IRSLHNKLLN AAQEREKDIK QEGETAICSE MTADRDPVYD ESTDEESENQ
TDLSGLASAA VSKDDSIISS LDVTDIAPSR KRRQRMQRNL GTEPKMAPQE NQLQEKEKPD
SSLPETSKKE HISAENMSLE TLRNSSPEDL FDEI*

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

176 / 176

Last intron/exon boundary

1068

Theoretical NMD boundary in CDS

842

Length of CDS

1005

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

131540

Chromosomal position

83209037

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