C2CD3 p.Phe628=
c.1884T>C · rs777025781 · VCV1595075
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0172%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · A>T here scores Δ0.31 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 3.5 | GERP 0.43, phastCons 0.99 |
| Overall | ||
| CADD | 9.989 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0172%
European (non-Finnish) · 202/1,174,650 alleles
Filtering AF
0.0152%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0144%
Overall
0.013%
208/1,599,934 alleles · ultra-rare
exomes 206/1,447,696 · genomes 2/152,238 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0172% | 5,815 |
| Remaining individualsnot grpmax-eligible | 0.00971% | 10,303 |
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
- C2CD3
- Protein
- p.Phe628=
- Coding
- c.1884T>C
- MANE Select
- NM_001286577
- dbSNP
- rs777025781
- Type
- single nucleotide variant
- Location
- chr11:74109112 (GRCh38)
- Gene constraint
- LOEUF 0.637 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 55.65
- Residue 628
- the c2 1 domain
Similar variants
- C2CD3 c.3911-2A>T Pathogenic/Likely pathogenic ★★ same type
- C2CD3 p.Arg621Ter Pathogenic/Likely pathogenic ★★ same type
- C2CD3 p.Arg666Ter Pathogenic ★★ same type
- C2CD3 p.Arg768Ter Pathogenic/Likely pathogenic ★★ same type
- C2CD3 p.Tyr173Ter Pathogenic/Likely pathogenic ★★ same type
- C2CD3 c.2085+5G>A Uncertain significance ★★ same type
- C2CD3 c.4951+6C>T Uncertain significance ★★ same type
- C2CD3 c.5495+4A>G 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/c2cd3-p-phe628 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown