rs1554660119
Variant summary
Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PM2PM5PP2PP3_Moderate
The ENST00000396594.8(GNE):āc.1085T>Gā(p.Val362Gly) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000692 in 1,445,706 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 Uncertain significance (ā ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V362A) has been classified as Pathogenic.
Frequency
Consequence
ENST00000396594.8 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GNE | NM_001128227.3 | c.1085T>G | p.Val362Gly | missense_variant | 6/12 | ENST00000396594.8 | NP_001121699.1 | |
GNE | NM_005476.7 | c.992T>G | p.Val331Gly | missense_variant | 6/12 | ENST00000642385.2 | NP_005467.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GNE | ENST00000396594.8 | c.1085T>G | p.Val362Gly | missense_variant | 6/12 | 1 | NM_001128227.3 | ENSP00000379839 | ||
GNE | ENST00000642385.2 | c.992T>G | p.Val331Gly | missense_variant | 6/12 | NM_005476.7 | ENSP00000494141 | P1 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD4 exome AF: 6.92e-7 AC: 1AN: 1445706Hom.: 0 Cov.: 27 AF XY: 0.00 AC XY: 0AN XY: 720398
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
GNE myopathy Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Counsyl | Jun 01, 2018 | - - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Mayo Clinic Laboratories, Mayo Clinic | Jul 16, 2024 | PP3, PM2, PM5 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at