chr16-1457295-T-A
Variant summary
Our verdict is Likely pathogenic. Variant got 9 ACMG points: 9P and 0B. PM1PM2PP3_StrongPP5
The NM_001287.6(CLCN7):c.781A>T(p.Ile261Phe) 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 Pathogenic (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. I261T) has been classified as Uncertain significance.
Frequency
Consequence
NM_001287.6 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 |
---|---|---|---|---|---|---|---|
CLCN7 | NM_001287.6 | c.781A>T | p.Ile261Phe | missense_variant | 9/25 | ENST00000382745.9 | |
CLCN7 | NM_001114331.3 | c.709A>T | p.Ile237Phe | missense_variant | 8/24 | ||
CLCN7 | XM_011522354.2 | c.607A>T | p.Ile203Phe | missense_variant | 9/25 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CLCN7 | ENST00000382745.9 | c.781A>T | p.Ile261Phe | missense_variant | 9/25 | 1 | NM_001287.6 | P1 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD4 exome Cov.: 32
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
Autosomal recessive osteopetrosis 4 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Jan 01, 2007 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at