rs121913046

Variant summary

Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PM2PP3_StrongPP5

The ENST00000285398.7(ERCC3):​c.355A>C​(p.Thr119Pro) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars).

Frequency

Genomes: not found (cov: 33)

Consequence

ERCC3
ENST00000285398.7 missense

Scores

13
5
1

Clinical Significance

Pathogenic no assertion criteria provided P:1

Conservation

PhyloP100: 8.02
Variant links:
Genes affected
ERCC3 (HGNC:3435): (ERCC excision repair 3, TFIIH core complex helicase subunit) This gene encodes an ATP-dependent DNA helicase that functions in nucleotide excision repair. The encoded protein is a subunit of basal transcription factor 2 (TFIIH) and, therefore, also functions in class II transcription. Mutations in this gene are associated with Xeroderma pigmentosum B, Cockayne's syndrome, and trichothiodystrophy. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2014]

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ACMG classification

Classification made for transcript

Verdict is Likely_pathogenic. Variant got 7 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.99
PP5
Variant 2-127292726-T-G is Pathogenic according to our data. Variant chr2-127292726-T-G is described in ClinVar as [Pathogenic]. Clinvar id is 16584.Status of the report is no_assertion_criteria_provided, 0 stars.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
ERCC3NM_000122.2 linkuse as main transcriptc.355A>C p.Thr119Pro missense_variant 3/15 ENST00000285398.7 NP_000113.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ERCC3ENST00000285398.7 linkuse as main transcriptc.355A>C p.Thr119Pro missense_variant 3/151 NM_000122.2 ENSP00000285398 P1

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Cov.:
33
GnomAD4 genome
Cov.:
33

ClinVar

Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link

Submissions by phenotype

Trichothiodystrophy 2, photosensitive Pathogenic:1
Pathogenic, no assertion criteria providedliterature onlyOMIMFeb 01, 1997- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.97
BayesDel_addAF
Pathogenic
0.45
D
BayesDel_noAF
Pathogenic
0.40
CADD
Pathogenic
32
DANN
Uncertain
1.0
DEOGEN2
Uncertain
0.76
D;.
Eigen
Pathogenic
0.95
Eigen_PC
Pathogenic
0.86
FATHMM_MKL
Uncertain
0.97
D
LIST_S2
Pathogenic
0.99
D;D
M_CAP
Pathogenic
0.54
D
MetaRNN
Pathogenic
0.99
D;D
MetaSVM
Uncertain
0.75
D
MutationAssessor
Pathogenic
3.7
H;.
MutationTaster
Benign
1.0
A;A
PrimateAI
Uncertain
0.72
T
PROVEAN
Pathogenic
-5.8
D;.
REVEL
Pathogenic
0.88
Sift
Pathogenic
0.0
D;.
Sift4G
Pathogenic
0.0010
D;.
Polyphen
1.0
D;.
Vest4
0.91
MutPred
0.96
Gain of methylation at K117 (P = 0.0758);Gain of methylation at K117 (P = 0.0758);
MVP
0.95
MPC
1.2
ClinPred
1.0
D
GERP RS
5.3
Varity_R
0.99
gMVP
0.90

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.030
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs121913046; hg19: chr2-128050302; API