CCDC112 p.Pro52Ser
c.154C>T · rs1454277660 · VCV2545697
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00223%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.06 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
| Constraint at this position | ||
| Conservation | phyloP -0.26 | GERP -4, phastCons 0.018 |
| Regional constraint | o/e 1.09 | unconstrained · MANE · 29 kb · p 0.025 · regional, not allelic |
| Overall | ||
| CADD | 4.578 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00223%
East Asian · 1/44,760 alleles
Overall
0.000124%
2/1,612,602 alleles · very rare
exomes 2/1,460,368 · genomes 0/152,234 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00223% | 44,760 |
| Admixed American | 0.00167% | 59,996 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- CCDC112
- Protein
- p.Pro52Ser
- Coding
- c.154C>T
- MANE Select
- NM_001040440
- dbSNP
- rs1454277660
- Type
- single nucleotide variant
- Location
- chr5:115284872 (GRCh38)
- Gene constraint
- LOEUF 0.875 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.18
Similar variants
- CCDC112 p.Ala165Val Uncertain significance ★ ⚠ same type
- CCDC112 p.Ala299Ser Uncertain significance ★ ⚠ same type
- CCDC112 p.Ala434Pro Uncertain significance ★ ⚠ same type
- CCDC112 p.Ala68Pro Uncertain significance ★ same type
- CCDC112 p.Arg391Cys Uncertain significance ★ ⚠ same type
- CCDC112 p.Arg391His Uncertain significance ★ ⚠ same type
- CCDC112 p.Arg391Leu Uncertain significance ★ ⚠ same type
- CCDC112 p.Arg393Leu Uncertain significance ★ ⚠ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/ccdc112-p-pro52ser (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown