CCDC47 p.Asp310=
c.930C>T · VCV3997036
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0134%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -5.1 | GERP -3.1 |
| Overall | ||
| CADD | 9.19 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0134%
East Asian · 6/44,890 alleles
Filtering AF
0.00579%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00394%
Overall
0.00174%
28/1,613,314 alleles · ultra-rare
exomes 24/1,461,028 · genomes 4/152,286 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0134% | 7,482 |
| Remaining individualsnot grpmax-eligible | 0.00961% | 10,410 |
| Admixed American | 0.005% | 20,003 |
| African / African-American | 0.00267% | 37,504 |
| Finnishnot grpmax-eligible | 0.00156% | 64,016 |
| South Asian | 0.0011% | 91,078 |
| European (non-Finnish) | 0.000763% | 131,031 |
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
- CCDC47
- Protein
- p.Asp310=
- Coding
- c.930C>T
- MANE Select
- NM_020198
- Type
- single nucleotide variant
- Location
- chr17:63756258 (GRCh38)
- Gene constraint
- LOEUF 0.918 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 77.07 · 1 PDB
- Residue 310
- a UniProt-annotated variant site (in thns; loss-of-function variant affecting er calcium ion homeostasis in patient cells; no protein detected by western blot in patient cells)
Similar variants
- CCDC47 p.Arg397Ter Pathogenic/Likely pathogenic ★★ same type
- CCDC47 p.Asp75Tyr Uncertain significance ★★ ⚠ same type
- CCDC47 p.Trp133Arg Uncertain significance ★★ ⚠ same type
- CCDC47 c.1093+112G>A Benign ★★ same type
- CCDC47 c.1094-3C>T Benign ★★ same type
- CCDC47 c.735+15C>T Benign ★★ same type
- CCDC47 p.Arg271Ter Likely pathogenic ★ same type
- CCDC47 c.669+5G>T 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/ccdc47-p-asp310 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown