CD1C p.Val318=
c.954C>A · rs36012320 · VCV716049
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.95%, 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 -20 | GERP -3.3 |
| Overall | ||
| CADD | 0.102 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.95%
African / African-American · 1,462/75,002 alleles
Filtering AF
1.87%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.83%
Overall
0.114%
1,847/1,613,956 alleles · low-frequency
exomes 1,010/1,461,688 · genomes 837/152,268 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.95% | 51 |
| Middle Eastern | 0.611% | 164 |
| Remaining individualsnot grpmax-eligible | 0.187% | 534 |
| Admixed American | 0.157% | 638 |
| Ashkenazi Jewishnot grpmax-eligible | 0.108% | 925 |
| South Asian | 0.011% | 9,108 |
| European (non-Finnish) | 0.00805% | 12,420 |
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
- CD1C
- Protein
- p.Val318=
- Coding
- c.954C>A
- MANE Select
- NM_001765
- dbSNP
- rs36012320
- Type
- single nucleotide variant
- Location
- chr1:158293276 (GRCh38)
- Gene constraint
- LOEUF 1.412 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 88.90 · 10 PDB
Similar variants
- CD1C p.Arg283Thr Likely benign ★★ same type
- CD1C p.Gln23= Benign ★★ same type
- CD1C p.Phe300Ser Benign ★★ same type
- CD1C p.Val282Leu Likely benign ★★ ⚠ same type
- CD1C p.Ala118Val Uncertain significance ★ ⚠ same type
- CD1C p.Arg187Gln Uncertain significance ★ ⚠ same type
- CD1C p.Arg213Cys Uncertain significance ★ ⚠ same type
- CD1C p.Arg281Leu 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/cd1c-p-val318 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown