rs34813378
Variant summary
Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PM2PP3_StrongPP5
The NM_001378156.1(C1QB):c.724G>A(p.Gly242Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000471 in 1,613,762 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 Pathogenic (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G242A) has been classified as Uncertain significance.
Frequency
Consequence
NM_001378156.1 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 | UniProt |
---|---|---|---|---|---|---|---|
C1QB | NM_001378156.1 | c.724G>A | p.Gly242Arg | missense_variant | 3/3 | ENST00000509305.6 | |
C1QB | NM_000491.5 | c.730G>A | p.Gly244Arg | missense_variant | 3/3 | ||
C1QB | NM_001371184.3 | c.724G>A | p.Gly242Arg | missense_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
C1QB | ENST00000509305.6 | c.724G>A | p.Gly242Arg | missense_variant | 3/3 | 1 | NM_001378156.1 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 151944Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000121 AC: 3AN: 248878Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 134852
GnomAD4 exome AF: 0.0000499 AC: 73AN: 1461818Hom.: 0 Cov.: 32 AF XY: 0.0000399 AC XY: 29AN XY: 727214
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 151944Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74190
ClinVar
Submissions by phenotype
C1Q deficiency Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Sep 28, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at