rs121912795
Variant summary
Our verdict is Likely pathogenic. Variant got 9 ACMG points: 9P and 0B. PM1PM2PM5PP3_ModeratePP5
The NM_001822.7(CHN1):c.668C>T(p.Ala223Val) 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. A223T) has been classified as Likely pathogenic.
Frequency
Consequence
NM_001822.7 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 |
---|---|---|---|---|---|---|---|
CHN1 | NM_001822.7 | c.668C>T | p.Ala223Val | missense_variant | 8/13 | ENST00000409900.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHN1 | ENST00000409900.9 | c.668C>T | p.Ala223Val | missense_variant | 8/13 | 1 | NM_001822.7 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1454406Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 722574
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Duane retraction syndrome 2 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Aug 08, 2008 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at