CCDC149 p.Val380Ile
c.1138G>A · rs1450849190 · VCV2597536
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00137%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.062 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.41 | GERP -0.76 |
| Regional constraint | o/e 0.88 | unconstrained · MANE · 104 kb · p 0.0018 · regional, not allelic |
| Overall | ||
| CADD | 7.452 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00137%
African / African-American · 1/73,168 alleles
Overall
7.15e-05%
1/1,399,416 alleles · very rare
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.Val380Ile
- Coding
- c.1138G>A
- MANE Select
- NM_001395273
- dbSNP
- rs1450849190
- Type
- single nucleotide variant
- Location
- chr4:24819898 (GRCh38)
- Gene constraint
- LOEUF 1.15 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 69.52
- Residue 380
- the 'disordered' region
Similar variants
- 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
- CCDC149 p.Arg145His 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-val380ile (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown