12-7070184-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 1P and 0B. PP3
The NM_001734.5(C1S):c.1600C>T(p.Arg534Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000118 in 1,614,016 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R534Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_001734.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
C1S | NM_001734.5 | c.1600C>T | p.Arg534Trp | missense_variant | 12/12 | ENST00000360817.10 | |
C1S | NM_201442.4 | c.1600C>T | p.Arg534Trp | missense_variant | 12/12 | ||
C1S | NM_001346850.2 | c.1099C>T | p.Arg367Trp | missense_variant | 11/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
C1S | ENST00000360817.10 | c.1600C>T | p.Arg534Trp | missense_variant | 12/12 | 1 | NM_001734.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000210 AC: 32AN: 152200Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000135 AC: 34AN: 251114Hom.: 0 AF XY: 0.000140 AC XY: 19AN XY: 135726
GnomAD4 exome AF: 0.000108 AC: 158AN: 1461816Hom.: 0 Cov.: 32 AF XY: 0.000114 AC XY: 83AN XY: 727206
GnomAD4 genome ? AF: 0.000210 AC: 32AN: 152200Hom.: 0 Cov.: 32 AF XY: 0.000215 AC XY: 16AN XY: 74350
ClinVar
Submissions by phenotype
not provided Uncertain:3
Uncertain significance, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Dec 01, 2021 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Oct 20, 2020 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Jan 25, 2024 | This sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 534 of the C1S protein (p.Arg534Trp). This variant is present in population databases (rs121909582, gnomAD 0.03%). This variant has not been reported in the literature in individuals affected with C1S-related conditions. ClinVar contains an entry for this variant (Variation ID: 17068). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt C1S protein function with a positive predictive value of 80%. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Complement component C1s deficiency;C4310681:Ehlers-Danlos syndrome, periodontal type 2 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | May 16, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at