rs1555575860
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PS1PM2PP3PP5
The NM_015386.3(COG4):c.1546G>C(p.Gly516Arg) 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). Another nucleotide change resulting in the same amino acid substitution has been previously reported as Pathogenic in Lovd.
Frequency
Consequence
NM_015386.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
COG4 | NM_015386.3 | c.1546G>C | p.Gly516Arg | missense_variant | Exon 12 of 19 | ENST00000323786.10 | NP_056201.2 | |
COG4 | NM_001195139.2 | c.1534G>C | p.Gly512Arg | missense_variant | Exon 12 of 18 | NP_001182068.2 | ||
COG4 | NM_001365426.1 | c.1120G>C | p.Gly374Arg | missense_variant | Exon 13 of 20 | NP_001352355.1 | ||
COG4 | NR_158212.1 | n.1505G>C | non_coding_transcript_exon_variant | Exon 12 of 19 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 32
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Microcephalic osteodysplastic dysplasia, Saul-Wilson type Pathogenic:1Other:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at