CIDEC p.Ser129=
c.387C>G · rs141361690 · VCV717831
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0133%, 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 1.1 | GERP -0.51, phastCons 1 |
| Overall | ||
| CADD | 6.07 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0133%
African / African-American · 10/75,006 alleles
Filtering AF
0.00722%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00549%
Overall
0.000681%
11/1,614,132 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0133% | 7,501 |
| Admixed American | 0.00167% | 60,014 |
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.Ser129=
- Coding
- c.387C>G
- MANE Select
- NM_001321142
- dbSNP
- rs141361690
- Type
- single nucleotide variant
- Location
- chr3:9870049 (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-ser129 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown