CCDC149 p.Val533Leu
c.1597G>T · rs193242333 · VCV2370251
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.349%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.009 | strongly benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -5.2 | GERP -3 |
| Regional constraint | o/e 0.88 | unconstrained · MANE · 104 kb · p 0.0018 · regional, not allelic |
| Overall | ||
| CADD | 0.004 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.349%
East Asian · 139/39,834 alleles
Filtering AF
0.302%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.284%
Overall
0.00993%
144/1,449,756 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.349% | 287 |
| Admixed American | 0.0117% | 8,579 |
| South Asian | 0.00152% | 65,636 |
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
- CCDC149
- Protein
- p.Val533Leu
- Coding
- c.1597G>T
- MANE Select
- NM_001395273
- dbSNP
- rs193242333
- Type
- single nucleotide variant
- Location
- chr4:24808400 (GRCh38)
- Gene constraint
- LOEUF 1.15 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 69.52
Similar variants
- CCDC149 p.Val533Met Uncertain significance ★ same residue
- CCDC149 c.48+17788T>A Uncertain significance ★ same type
- CCDC149 c.48+17796A>G Uncertain significance ★ same type
- CCDC149 c.48+17799G>A Uncertain significance ★ same type
- CCDC149 c.48+17811A>T Uncertain significance ★ same type
- CCDC149 p.Ala412Val Uncertain significance ★ same type
- CCDC149 p.Ala420Thr Uncertain significance ★ same type
- CCDC149 p.Arg110Ser 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/ccdc149-p-val533leu (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown