X-50072553-G-T
Variant summary
Our verdict is Likely pathogenic. Variant got 9 ACMG points: 9P and 0B. PM2PM5PP3_StrongPP5
The NM_001127898.4(CLCN5):c.380G>T(p.Gly127Val) 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 ClinVar as Pathogenic (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G127R) has been classified as Likely pathogenic.
Frequency
Consequence
NM_001127898.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CLCN5 | NM_001127898.4 | c.380G>T | p.Gly127Val | missense_variant | 6/15 | ENST00000376091.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CLCN5 | ENST00000376091.8 | c.380G>T | p.Gly127Val | missense_variant | 6/15 | 2 | NM_001127898.4 | P3 |
Frequencies
GnomAD3 genomes Cov.: 22
GnomAD4 exome Cov.: 28
GnomAD4 genome Cov.: 22
ClinVar
Submissions by phenotype
X-linked recessive nephrolithiasis with renal failure Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | May 01, 1998 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at