chrX-49235685-A-C
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PM5PP3_Moderate
The NM_014008.5(CCDC22):c.49A>C(p.Thr17Pro) variant causes a missense, splice region change. The variant was absent in control chromosomes in GnomAD project. 2/3 splice prediction tools predicting alterations to normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T17A) has been classified as Pathogenic.
Frequency
Consequence
NM_014008.5 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCDC22 | NM_014008.5 | c.49A>C | p.Thr17Pro | missense_variant, splice_region_variant | 1/17 | ENST00000376227.4 | |
CCDC22 | XM_005272599.5 | c.49A>C | p.Thr17Pro | missense_variant, splice_region_variant | 1/17 | ||
CCDC22 | XR_430506.4 | n.216A>C | splice_region_variant, non_coding_transcript_exon_variant | 1/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC22 | ENST00000376227.4 | c.49A>C | p.Thr17Pro | missense_variant, splice_region_variant | 1/17 | 1 | NM_014008.5 | P1 | |
CCDC22 | ENST00000496651.5 | n.190A>C | splice_region_variant, non_coding_transcript_exon_variant | 1/6 | 3 |
Frequencies
GnomAD3 genomes Cov.: 22
GnomAD4 exome Cov.: 30
GnomAD4 genome Cov.: 22
ClinVar
Submissions by phenotype
Ritscher-Schinzel syndrome 2 Uncertain:1
Uncertain significance, criteria provided, single submitter | research | Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development | Jan 01, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.