CCDC138 p.Ser119=
c.357G>A · rs36034137 · VCV2651256
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.832%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.012 | strongly benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.055 | GERP -1.1, phastCons 0.14 |
| Overall | ||
| CADD | 10.61 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.832%
African / African-American · 620/74,482 alleles
Filtering AF
0.778%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.757%
Overall
0.0884%
1,413/1,599,060 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.832% | 120 |
| Remaining individualsnot grpmax-eligible | 0.108% | 925 |
| Admixed American | 0.0914% | 1,094 |
| European (non-Finnish) | 0.0514% | 1,945 |
| Middle Eastern | 0.05% | 2,001 |
| Finnishnot grpmax-eligible | 0.0429% | 2,331 |
| South Asian | 0.035% | 2,861 |
| East Asian | 0.0202% | 4,955 |
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
- CCDC138
- Protein
- p.Ser119=
- Coding
- c.357G>A
- MANE Select
- NM_144978
- dbSNP
- rs36034137
- Type
- single nucleotide variant
- Location
- chr2:108791765 (GRCh38)
- Gene constraint
- LOEUF 0.915 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 73.25
Similar variants
- CCDC138 p.Ala133Val Uncertain significance ★ ⚠ same type
- CCDC138 p.Ala166Thr Uncertain significance ★ ⚠ same type
- CCDC138 p.Ala340Thr Uncertain significance ★ ⚠ same type
- CCDC138 p.Ala482Thr Uncertain significance ★ ⚠ same type
- CCDC138 p.Ala663Thr Uncertain significance ★ ⚠ same type
- CCDC138 p.Arg142Ser Uncertain significance ★ ⚠ same type
- CCDC138 p.Arg170Trp Uncertain significance ★ ⚠ same type
- CCDC138 p.Arg210His 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/ccdc138-p-ser119 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown