CD109 p.Val1263=
c.3789G>A · rs59555720 · VCV776137
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Common
common (popmax 8.07%, afr) — too common for a highly-penetrant pathogenic allele
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>T here scores Δ0.21 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 5 | GERP 1.9, phastCons 1 |
| Overall | ||
| CADD | 10.83 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.07%
African / African-American · 5,718/70,890 alleles
Filtering AF
7.89%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 7.82%
Overall
0.417%
6,502/1,559,480 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 8.07% | 12 |
| Admixed American | 0.662% | 151 |
| Remaining individualsnot grpmax-eligible | 0.536% | 187 |
| Middle Eastern | 0.448% | 223 |
| South Asian | 0.0148% | 6,748 |
| European (non-Finnish) | 0.0112% | 8,948 |
| East Asian | 0.00234% | 42,646 |
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
- CD109
- Protein
- p.Val1263=
- Coding
- c.3789G>A
- MANE Select
- NM_133493
- dbSNP
- rs59555720
- Type
- single nucleotide variant
- Location
- chr6:73815001 (GRCh38)
- Gene constraint
- LOEUF 1.092 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.42 · 3 PDB
- Residue 1263
- a β-strand
Similar variants
- CD109 p.Gln416Glu Likely benign ★★ same type
- CD109 p.Ile206Val Benign ★★ ⚠ same type
- CD109 p.Ala1104Val Uncertain significance ★ ⚠ same type
- CD109 p.Ala1115Gly Uncertain significance ★ ⚠ same type
- CD109 p.Ala1148Gly Uncertain significance ★ ⚠ same type
- CD109 p.Ala1190Pro Uncertain significance ★ ⚠ same type
- CD109 p.Ala1196Asp Uncertain significance ★ ⚠ same type
- CD109 p.Ala1196Val 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/cd109-p-val1263 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown