19-55898809-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_176810.2(NLRP13):c.2918G>A(p.Cys973Tyr) variant causes a missense change involving the alteration of a non-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 Uncertain significance (★).
Frequency
Consequence
NM_176810.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NLRP13 | ENST00000342929.4 | c.2918G>A | p.Cys973Tyr | missense_variant | Exon 10 of 11 | 1 | NM_176810.2 | ENSP00000343891.3 | ||
NLRP13 | ENST00000588751.5 | c.2918G>A | p.Cys973Tyr | missense_variant | Exon 10 of 12 | 5 | ENSP00000467899.1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome Cov.: 30
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2918G>A (p.C973Y) alteration is located in exon 10 (coding exon 10) of the NLRP13 gene. This alteration results from a G to A substitution at nucleotide position 2918, causing the cysteine (C) at amino acid position 973 to be replaced by a tyrosine (Y). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.