rs879255581
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PM2PM5PP2PP3_StrongPP5_Moderate
The NM_001830.4(CLCN4):c.662T>C(p.Leu221Pro) 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. 12/20 in silico tools predict a damaging outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. L221V) has been classified as Pathogenic.
Frequency
Consequence
NM_001830.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CLCN4 | NM_001830.4 | c.662T>C | p.Leu221Pro | missense_variant | 7/13 | ENST00000380833.9 | |
CLCN4 | NM_001256944.2 | c.380T>C | p.Leu127Pro | missense_variant | 5/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CLCN4 | ENST00000380833.9 | c.662T>C | p.Leu221Pro | missense_variant | 7/13 | 1 | NM_001830.4 | P4 |
Frequencies
GnomAD3 genomes ? Cov.: 23
GnomAD4 exome Cov.: 31
GnomAD4 genome ? Cov.: 23
ClinVar
Submissions by phenotype
CLCN4-related disorder Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Sydney Children's Hospital, SCHN | Mar 22, 2016 | De novo variant. Clinical phenotype consistent with case series of individuals with CLCN4 related disorder. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at