C2CD2L p.Arg71=
c.211C>A · rs561120047 · VCV724766
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.617%, afr)
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 1.7 | GERP -1.5, phastCons 1 |
| Overall | ||
| CADD | 12.77 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.617%
African / African-American · 427/69,188 alleles
Filtering AF
0.569%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.55%
Overall
0.0305%
472/1,546,398 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.617% | 162 |
| Admixed American | 0.0423% | 2,367 |
| Remaining individualsnot grpmax-eligible | 0.0338% | 2,958 |
| South Asian | 0.00118% | 84,948 |
| European (non-Finnish) | 0.000347% | 288,554 |
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
- C2CD2L
- Protein
- p.Arg71=
- Coding
- c.211C>A
- MANE Select
- NM_001290474
- dbSNP
- rs561120047
- Type
- single nucleotide variant
- Location
- chr11:119107952 (GRCh38)
- Gene constraint
- LOEUF 0.494 · pLI 0.98 (gnomAD)
- Structure
- AlphaFold pLDDT 64.75 · 1 PDB
Similar variants
- C2CD2L c.451-8G>A Benign ★★ same type
- C2CD2L p.Ala14Thr Uncertain significance ★ ⚠ same type
- C2CD2L p.Ala173Thr Uncertain significance ★ ⚠ same type
- C2CD2L p.Ala245Ser Uncertain significance ★ ⚠ same type
- C2CD2L p.Ala245Thr Uncertain significance ★ ⚠ same type
- C2CD2L p.Ala326Val Uncertain significance ★ ⚠ same type
- C2CD2L p.Ala512Val Uncertain significance ★ ⚠ same type
- C2CD2L p.Ala524Thr 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/c2cd2l-p-arg71 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown