rs267606965
Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM1PP3_ModeratePP5
The NM_013382.7(POMT2):c.1117G>T(p.Val373Phe) variant causes a missense, splice region change. In-silico tool predicts a pathogenic outcome for this variant. 2/2 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Pathogenic (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V373L) has been classified as Uncertain significance.
Frequency
Consequence
NM_013382.7 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
POMT2 | NM_013382.7 | c.1117G>T | p.Val373Phe | missense_variant, splice_region_variant | 10/21 | ENST00000261534.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
POMT2 | ENST00000261534.9 | c.1117G>T | p.Val373Phe | missense_variant, splice_region_variant | 10/21 | 1 | NM_013382.7 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 25
GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 1406976Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 691420
GnomAD4 genome ? Cov.: 25
ClinVar
Submissions by phenotype
Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A2 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Oct 01, 2007 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at