CCDC137 p.Ala166=
c.498G>A · VCV3828148
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0176%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 1.8 | GERP -1.4, phastCons 1 |
| Overall | ||
| CADD | 13.62 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0176%
South Asian · 16/90,918 alleles
Filtering AF
0.011%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.009%
Overall
0.00167%
27/1,612,212 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0176% | 5,682 |
| Middle Eastern | 0.0164% | 6,084 |
| East Asian | 0.00223% | 44,850 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,454 |
| European (non-Finnish) | 0.000678% | 147,459 |
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
- CCDC137
- Protein
- p.Ala166=
- Coding
- c.498G>A
- MANE Select
- NM_199287
- Type
- single nucleotide variant
- Location
- chr17:81671744 (GRCh38)
- Gene constraint
- LOEUF 1.308 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 74.94
- Residue 166
- the 'disordered' region
Similar variants
- CCDC137 p.Arg247Cys Uncertain significance ★★ ⚠ same type
- CCDC137 p.Ala144Thr Uncertain significance ★ ⚠ same type
- CCDC137 p.Ala261Val Uncertain significance ★ ⚠ same type
- CCDC137 p.Ala2Ser Uncertain significance ★ ⚠ same type
- CCDC137 p.Ala2Val Uncertain significance ★ ⚠ same type
- CCDC137 p.Ala9Glu Uncertain significance ★ ⚠ same type
- CCDC137 p.Ala9Val Uncertain significance ★ ⚠ same type
- CCDC137 p.Arg12Ser 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/ccdc137-p-ala166 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown