DIAPH3 p.Val913=
c.2739C>G · rs375809462 · VCV1199980
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0614%, afr)
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 6.6 | GERP 1.8, phastCons 1 |
| Overall | ||
| CADD | 13.4 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0614%
African / African-American · 46/74,898 alleles
Filtering AF
0.0472%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0423%
Overall
0.0036%
58/1,612,676 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0614% | 1,628 |
| Admixed American | 0.0133% | 7,491 |
| Remaining individualsnot grpmax-eligible | 0.00481% | 20,809 |
| European (non-Finnish) | 8.48e-05% | 1,179,409 |
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
- DIAPH3
- Protein
- p.Val913=
- Coding
- c.2739C>G
- MANE Select
- NM_001042517
- dbSNP
- rs375809462
- Type
- single nucleotide variant
- Location
- chr13:59839447 (GRCh38)
- Gene constraint
- LOEUF 0.889 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 72.33 · 2 PDB
- Residue 913
- the fh2 domain
Similar variants
- DIAPH3 p.Ala500Val Uncertain significance ★★ ⚠ same type
- DIAPH3 p.Ala546Thr Uncertain significance ★★ ⚠ same type
- DIAPH3 p.Arg1027His Uncertain significance ★★ ⚠ same type
- DIAPH3 p.Arg1048Cys Uncertain significance ★★ ⚠ same type
- DIAPH3 p.Arg1048Gly Uncertain significance ★★ ⚠ same type
- DIAPH3 p.Arg1089Pro Uncertain significance ★★ ⚠ same type
- DIAPH3 p.Arg1191Ter Uncertain significance ★★ same type
- DIAPH3 p.Arg31Gln 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/diaph3-p-val913 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown