rs67394386
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PM1PM2PM5PP2PP3_StrongPP5
The NM_000088.4(COL1A1):c.3226G>T(p.Gly1076Cys) 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 Lovd as Pathogenic (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G1076S) has been classified as Likely pathogenic.
Frequency
Consequence
NM_000088.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL1A1 | NM_000088.4 | c.3226G>T | p.Gly1076Cys | missense_variant | 44/51 | ENST00000225964.10 | |
COL1A1 | XM_011524341.2 | c.3028G>T | p.Gly1010Cys | missense_variant | 41/48 | ||
COL1A1 | XM_005257058.5 | c.2956G>T | p.Gly986Cys | missense_variant | 42/49 | ||
COL1A1 | XM_005257059.5 | c.2308G>T | p.Gly770Cys | missense_variant | 31/38 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL1A1 | ENST00000225964.10 | c.3226G>T | p.Gly1076Cys | missense_variant | 44/51 | 1 | NM_000088.4 | P1 | |
COL1A1 | ENST00000486572.1 | n.424G>T | non_coding_transcript_exon_variant | 1/2 | 3 | ||||
COL1A1 | ENST00000511732.1 | n.550G>T | non_coding_transcript_exon_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 36
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at