CIDEC p.Val201=
c.603A>G · rs201404178 · VCV726948
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.466%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.076 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.87 | GERP -1.6, phastCons 1 |
| Overall | ||
| CADD | 3.378 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.466%
East Asian · 209/44,876 alleles
Filtering AF
0.414%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.394%
Overall
0.0287%
463/1,614,144 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.466% | 215 |
| Remaining individualsnot grpmax-eligible | 0.0944% | 1,059 |
| South Asian | 0.0834% | 1,199 |
| African / African-American | 0.0187% | 5,362 |
| Middle Eastern | 0.0165% | 6,048 |
| European (non-Finnish) | 0.00856% | 11,683 |
| Admixed American | 0.00333% | 30,009 |
| Finnishnot grpmax-eligible | 0.00156% | 64,010 |
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
- CIDEC
- Protein
- p.Val201=
- Coding
- c.603A>G
- MANE Select
- NM_001321142
- dbSNP
- rs201404178
- Type
- single nucleotide variant
- Location
- chr3:9867248 (GRCh38)
- Gene constraint
- LOEUF 0.927 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 74.19
Similar variants
- CIDEC p.Arg182His Uncertain significance ★★ ⚠ same type
- CIDEC p.Ile156Thr Uncertain significance ★★ ⚠ same type
- CIDEC p.Met195Ile Uncertain significance ★★ ⚠ same type
- CIDEC p.Val54Met Uncertain significance ★★ ⚠ same type
- CIDEC c.207+180G>A Benign ★★ same type
- CIDEC c.208-91C>T Benign ★★ same type
- CIDEC c.53+77T>A Benign ★★ same type
- CIDEC c.-25-52G>T Benign ★★ 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/cidec-p-val201 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown