CCDC149 p.Phe379Ile
c.1135T>A · rs369908357 · VCV2601045
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.149%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.15 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 2.2 | GERP 0.53, phastCons 1 |
| Regional constraint | o/e 0.88 | unconstrained · MANE · 104 kb · p 0.0018 · regional, not allelic |
| Overall | ||
| CADD | 19.42 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.149%
African / African-American · 109/73,098 alleles
Filtering AF
0.126%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.118%
Overall
0.00735%
114/1,551,498 alleles · rare
exomes 59/1,399,424 · genomes 55/152,074 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.149% | 671 |
| Remaining individualsnot grpmax-eligible | 0.00832% | 12,025 |
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.Phe379Ile
- Coding
- c.1135T>A
- MANE Select
- NM_001395273
- dbSNP
- rs369908357
- Type
- single nucleotide variant
- Location
- chr4:24819901 (GRCh38)
- Gene constraint
- LOEUF 1.15 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 69.52
- Residue 379
- 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-phe379ile (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown