CCDC149 p.Ala412Val
c.1235C>T · rs200984075 · VCV2349449
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0501%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.063 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 1.3 | GERP -0.29, phastCons 0.009 |
| Regional constraint | o/e 0.88 | unconstrained · MANE · 104 kb · p 0.0018 · regional, not allelic |
| Overall | ||
| CADD | 17.12 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0501%
Middle Eastern · 3/5,994 alleles
Filtering AF
0.0369%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0357%
Overall
0.0322%
500/1,551,896 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0501% | 1,998 |
| European (non-Finnish) | 0.0399% | 2,504 |
| Remaining individualsnot grpmax-eligible | 0.0266% | 3,760 |
| South Asian | 0.0131% | 7,641 |
| Admixed American | 0.0098% | 10,199 |
| African / African-American | 0.0082% | 12,193 |
| East Asian | 0.00244% | 40,910 |
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.Ala412Val
- Coding
- c.1235C>T
- MANE Select
- NM_001395273
- dbSNP
- rs200984075
- Type
- single nucleotide variant
- Location
- chr4:24808762 (GRCh38)
- Gene constraint
- LOEUF 1.15 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 69.52
- Residue 412
- 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.Ala420Thr Uncertain significance ★ same type
- CCDC149 p.Arg110Ser Uncertain significance ★ same type
- CCDC149 p.Arg145His Uncertain significance ★ same type
- CCDC149 p.Arg154Gln 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-ala412val (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown