CCDC149 p.Arg58Cys
c.172C>T · VCV3486100
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00223%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.22 | benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 6.5 | GERP 0.68, phastCons 1 |
| Regional constraint | o/e 0.88 | unconstrained · MANE · 104 kb · p 0.0018 · regional, not allelic |
| Overall | ||
| CADD | 32.0 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00223%
East Asian · 1/44,882 alleles
Filtering AF
0.000365%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000137%
Overall
0.00031%
5/1,613,870 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00223% | 44,882 |
| South Asian | 0.0022% | 45,527 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,478 |
| European (non-Finnish) | 8.48e-05% | 1,179,935 |
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.Arg58Cys
- Coding
- c.172C>T
- MANE Select
- NM_001395273
- Type
- single nucleotide variant
- Location
- chr4:24876574 (GRCh38)
- Gene constraint
- LOEUF 1.15 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 69.52
Similar variants
- CCDC149 p.Arg58His 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-arg58cys (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown