TIMCC p.Val218=
c.654G>A · rs753344193 · VCV3034539
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0822%, mid)
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 0.74 | GERP 0.98, phastCons 1 |
| Overall | ||
| CADD | 12.08 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0822%
Middle Eastern · 5/6,082 alleles
Filtering AF
0.0323%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.021%
Overall
0.00737%
119/1,613,922 alleles · ultra-rare
exomes 116/1,461,698 · genomes 3/152,224 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0822% | 1,216 |
| South Asian | 0.0132% | 7,590 |
| European (non-Finnish) | 0.00814% | 12,291 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,824 |
| African / African-American | 0.004% | 24,972 |
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
- TIMCC
- Protein
- p.Val218=
- Coding
- c.654G>A
- MANE Select
- NM_001329752
- dbSNP
- rs753344193
- Type
- single nucleotide variant
- Location
- chr2:70297373 (GRCh38)
- Structure
- AlphaFold pLDDT 95.42
Similar variants
- TIMCC p.Asn24= Benign/Likely benign ★★ same type
- FAM136A p.Gln183Ter Pathogenic ★ same type
- FAM136A p.Ala12Val Uncertain significance ★ ⚠ same type
- FAM136A p.Ala144Thr Uncertain significance ★ same type
- FAM136A p.Ala203Asp Uncertain significance ★ ⚠ same type
- FAM136A p.Ala2Val Uncertain significance ★ ⚠ same type
- FAM136A p.Arg163Gly Uncertain significance ★ ⚠ same type
- FAM136A p.Gln10His 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/timcc-p-val218 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown