3-7578930-C-A
Variant summary
Our verdict is Likely pathogenic. Variant got 9 ACMG points: 9P and 0B. PM1PM2PP3_StrongPP5
The NM_000844.4(GRM7):c.2024C>A(p.Thr675Lys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,870 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 12/21 in silico tools predict a damaging outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (no stars). Synonymous variant affecting the same amino acid position (i.e. T675T) has been classified as Likely benign.
Frequency
Consequence
NM_000844.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GRM7 | NM_000844.4 | c.2024C>A | p.Thr675Lys | missense_variant | 8/10 | ENST00000357716.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GRM7 | ENST00000357716.9 | c.2024C>A | p.Thr675Lys | missense_variant | 8/10 | 1 | NM_000844.4 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461870Hom.: 0 Cov.: 35 AF XY: 0.00 AC XY: 0AN XY: 727234
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Hypotonia;C0036572:Seizure;C0557874:Global developmental delay;C3714756:Intellectual disability;C4025616:CNS hypomyelination;C4551584:Brain atrophy Pathogenic:1
Likely pathogenic, no assertion criteria provided | research | Lupski Lab, Baylor-Hopkins CMG, Baylor College of Medicine | Jan 10, 2016 | - - |
Neurodevelopmental disorder with seizures, hypotonia, and brain imaging abnormalities Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Sep 11, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at