CIDEC p.Thr198=
c.594A>G · rs147072100 · VCV434767
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0827%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.194 | benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -5.3 | GERP -3.7 |
| Overall | ||
| CADD | 0.083 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0827%
Middle Eastern · 5/6,048 alleles
Filtering AF
0.0339%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0327%
Overall
0.0308%
497/1,614,142 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0827% | 1,210 |
| European (non-Finnish) | 0.0368% | 2,719 |
| South Asian | 0.0285% | 3,503 |
| Remaining individualsnot grpmax-eligible | 0.0224% | 4,465 |
| Finnishnot grpmax-eligible | 0.0141% | 7,110 |
| East Asian | 0.00668% | 14,964 |
| Admixed American | 0.005% | 20,009 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,608 |
| African / African-American | 0.00266% | 37,536 |
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.Thr198=
- Coding
- c.594A>G
- MANE Select
- NM_001321142
- dbSNP
- rs147072100
- Type
- single nucleotide variant
- Location
- chr3:9867257 (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-thr198 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown