Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0823%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.09 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.39 | GERP 0.82, phastCons 0.99 |
| Overall | ||
| CADD | 6.543 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0823%
Middle Eastern · 5/6,072 alleles
Filtering AF
0.0324%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0236%
Overall
0.0233%
376/1,614,058 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0823% | 1,214 |
| European (non-Finnish) | 0.027% | 3,699 |
| South Asian | 0.0252% | 3,961 |
| Remaining individualsnot grpmax-eligible | 0.0224% | 4,463 |
| East Asian | 0.0134% | 7,484 |
| Admixed American | 0.01% | 10,001 |
| African / African-American | 0.00267% | 37,475 |
| Finnishnot grpmax-eligible | 0.00156% | 63,996 |
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.Gln196=
- Coding
- c.588G>A
- MANE Select
- NM_001321142
- dbSNP
- rs1132704
- Type
- single nucleotide variant
- Location
- chr3:9867263 (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-gln196 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown