Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 5 submitters
gnomAD v4.1
Common
common (popmax 46.7%, afr) — too common for a highly-penetrant pathogenic allele
Conditions
1
CIDEC-related familial partial lipodystrophy
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 2.1 | GERP -0.88, phastCons 0.97 |
| Overall | ||
| CADD | 8.474 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
46.7%
African / African-American · 34,153/73,080 alleles
Filtering AF
46.3%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 46.1%
Overall
22.4%
347,934/1,550,738 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 46.7% | 2 |
| Admixed American | 33.7% | 3 |
| Ashkenazi Jewishnot grpmax-eligible | 24.5% | 4 |
| Finnishnot grpmax-eligible | 24.4% | 4 |
| East Asian | 24.1% | 4 |
| South Asian | 23.7% | 4 |
| Remaining individualsnot grpmax-eligible | 22.7% | 4 |
| Amishnot grpmax-eligible | 21.9% | 5 |
| Middle Eastern | 21.6% | 5 |
| European (non-Finnish) | 20.1% | 5 |
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.Leu32=
- Coding
- c.96G>T
- MANE Select
- NM_001321142
- dbSNP
- rs456168
- Type
- single nucleotide variant
- Location
- chr3:9877177 (GRCh38)
- Gene constraint
- LOEUF 0.927 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 74.19
- Residue 32
- the 'required for liquid-liquid phase separation (llps)' region
Disease context
CIDEC-related familial partial lipodystrophy — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor CIDEC-related familial partial lipodystrophy (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Adolescent
- Prevalence
- <1 / 1 000 000 (Worldwide)
Similar variants
- CIDEC p.Glu186Ter Pathogenic same condition
- CIDEC p.Gln211fs Likely pathogenic ★ same condition
- CIDEC p.Gly204fs Likely pathogenic ★ same condition
- CIDEC p.Lys223fs Uncertain significance ★ same condition
- 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
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-leu32 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown