12-7086423-C-A
Variant summary
Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PS1_ModeratePM1PM2PM5PP5_Moderate
The NM_001733.7(C1R):c.1073G>T(p.Cys358Phe) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (★). Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely pathogenic in UniProt. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. C358Y) has been classified as Pathogenic.
Frequency
Consequence
NM_001733.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 10 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
C1R | ENST00000647956.2 | c.1073G>T | p.Cys358Phe | missense_variant | 8/11 | NM_001733.7 | ENSP00000497341.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 0
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Ehlers-Danlos syndrome, periodontal type 1 Pathogenic:2
Pathogenic, criteria provided, single submitter | research | Institute of Human Genetics, Medical University Innsbruck | Aug 23, 2016 | - - |
Pathogenic, no assertion criteria provided | literature only | OMIM | Oct 31, 2016 | - - |
Ehlers-Danlos syndrome, periodontal type 2 Pathogenic:1
Likely pathogenic, no assertion criteria provided | research | University of Washington Center for Mendelian Genomics, University of Washington | Oct 13, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at