12-65278770-T-G
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Variant summary
Our verdict is Pathogenic. Variant got 14 ACMG points: 14P and 0B. PVS1PS1_ModeratePM2PP5_Moderate
The ENST00000355192.8(MSRB3):āc.2T>Gā(p.Met1?) variant causes a start lost change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000114 in 1,577,848 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (ā ).
Frequency
Genomes: š 0.000013 ( 0 hom., cov: 32)
Exomes š: 0.000011 ( 0 hom. )
Consequence
MSRB3
ENST00000355192.8 start_lost
ENST00000355192.8 start_lost
Scores
3
2
11
Clinical Significance
Conservation
PhyloP100: 0.559
Genes affected
MSRB3 (HGNC:27375): (methionine sulfoxide reductase B3) The protein encoded by this gene catalyzes the reduction of methionine sulfoxide to methionine. This enzyme acts as a monomer and requires zinc as a cofactor. Several transcript variants encoding two different isoforms have been found for this gene. One of the isoforms localizes to mitochondria while the other localizes to endoplasmic reticula. [provided by RefSeq, Jul 2010]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 14 ACMG points.
PVS1
Start lost variant, no new inframe start found.
PS1
Another start lost variant in ENST00000355192.8 (MSRB3) was described as [Conflicting_classifications_of_pathogenicity] in ClinVar as 1699605
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 12-65278770-T-G is Pathogenic according to our data. Variant chr12-65278770-T-G is described in ClinVar as [Likely_pathogenic]. Clinvar id is 1324742.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MSRB3 | NM_001031679.3 | c.-147T>G | 5_prime_UTR_variant | 1/7 | ENST00000308259.10 | NP_001026849.1 | ||
MSRB3 | NM_198080.4 | c.2T>G | p.Met1? | start_lost | 1/6 | NP_932346.1 | ||
MSRB3 | NM_001193460.2 | c.-311T>G | 5_prime_UTR_variant | 1/8 | NP_001180389.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MSRB3 | ENST00000308259.10 | c.-147T>G | 5_prime_UTR_variant | 1/7 | 1 | NM_001031679.3 | ENSP00000312274 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 152078Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000105 AC: 2AN: 189636Hom.: 0 AF XY: 0.0000196 AC XY: 2AN XY: 102108
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GnomAD4 exome AF: 0.0000112 AC: 16AN: 1425770Hom.: 0 Cov.: 31 AF XY: 0.0000170 AC XY: 12AN XY: 705912
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GnomAD4 genome AF: 0.0000132 AC: 2AN: 152078Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74274
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ClinVar
Significance: Likely pathogenic
Submissions summary: Pathogenic:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Autosomal recessive nonsyndromic hearing loss 74 Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Aug 04, 2020 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Benign
T;T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Uncertain
D;D
M_CAP
Pathogenic
D
MetaRNN
Pathogenic
D;D
MetaSVM
Benign
T
MutationTaster
Benign
D;D;N;N
PROVEAN
Benign
N;N
REVEL
Benign
Sift
Pathogenic
D;D
Sift4G
Uncertain
D;D
Polyphen
B;.
Vest4
MutPred
Gain of MoRF binding (P = 0.0092);Gain of MoRF binding (P = 0.0092);
MVP
ClinPred
T
GERP RS
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gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at