chrX-49237162-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_014008.5(CCDC22):c.127C>T(p.Arg43Cys) variant causes a missense change. The variant allele was found at a frequency of 0.000000911 in 1,097,458 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 hemizygotes in GnomAD. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R43P) has been classified as Uncertain significance.
Frequency
Consequence
NM_014008.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCDC22 | NM_014008.5 | c.127C>T | p.Arg43Cys | missense_variant | 2/17 | ENST00000376227.4 | |
CCDC22 | XM_005272599.5 | c.127C>T | p.Arg43Cys | missense_variant | 2/17 | ||
CCDC22 | XR_430506.4 | n.294C>T | non_coding_transcript_exon_variant | 2/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC22 | ENST00000376227.4 | c.127C>T | p.Arg43Cys | missense_variant | 2/17 | 1 | NM_014008.5 | P1 | |
CCDC22 | ENST00000490300.1 | n.270C>T | non_coding_transcript_exon_variant | 1/5 | 3 | ||||
CCDC22 | ENST00000496651.5 | n.268C>T | non_coding_transcript_exon_variant | 2/6 | 3 |
Frequencies
GnomAD3 genomes Cov.: 24
GnomAD4 exome AF: 9.11e-7 AC: 1AN: 1097458Hom.: 0 Cov.: 31 AF XY: 0.00000276 AC XY: 1AN XY: 362836
GnomAD4 genome Cov.: 24
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Dec 11, 2023 | Variant summary: CCDC22 c.127C>T (p.Arg43Cys) results in a non-conservative amino acid change located in the CCDC22, N-terminal domain (IPR048349) of the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant was absent in 182820 control chromosomes. The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. To our knowledge, no occurrence of c.127C>T in individuals affected with Ritscher-Schinzel Syndrome 2 and no experimental evidence demonstrating its impact on protein function have been reported. No submitters have cited clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as uncertain significance. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.