CCDC112 p.Arg51Cys
c.151C>T · VCV4648930
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.011%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| REVEL | 0.082 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | Δ0.22 | acceptor gain · deltas |
| Pangolin | Δ0.23 | gain · loss 0.08 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 6.6 | GERP 1.1, phastCons 1 |
| Regional constraint | o/e 1.09 | unconstrained · MANE · 29 kb · p 0.025 · regional, not allelic |
| Overall | ||
| CADD | 27.2 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.011%
South Asian · 10/90,936 alleles
Filtering AF
0.00595%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00454%
Overall
0.00205%
33/1,612,324 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.011% | 9,094 |
| African / African-American | 0.00267% | 37,437 |
| Admixed American | 0.00167% | 59,966 |
| European (non-Finnish) | 0.00161% | 62,046 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,406 |
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.Arg51Cys
- Coding
- c.151C>T
- MANE Select
- NM_001040440
- Type
- single nucleotide variant
- Location
- chr5:115284875 (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-arg51cys (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown