DNAAF4 p.Thr303=
c.909G>A · rs138026922 · VCV1009482
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0281%, 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 -1.4 | GERP -3.4, phastCons 0.001 |
| Overall | ||
| CADD | 8.201 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0281%
South Asian · 24/85,360 alleles
Filtering AF
0.0194%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0164%
Overall
0.00548%
87/1,586,786 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0281% | 3,557 |
| East Asian | 0.0158% | 6,310 |
| European (non-Finnish) | 0.00461% | 21,695 |
| Admixed American | 0.00191% | 52,306 |
| Remaining individualsnot grpmax-eligible | 0.00163% | 61,342 |
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
- DNAAF4
- Protein
- p.Thr303=
- Coding
- c.909G>A
- MANE Select
- NM_130810
- dbSNP
- rs138026922
- Type
- single nucleotide variant
- Location
- chr15:55435043 (GRCh38)
- Gene constraint
- LOEUF 1.018 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 84.00
Similar variants
- DNAAF4 p.Thr303Met Conflicting classifications of pathogenicity ★ ⚠ same residue
- DNAAF4 c.1047+1G>A Pathogenic/Likely pathogenic ★★ same type
- DNAAF4 c.1153+1G>A Pathogenic ★★ same type
- DNAAF4 c.405+1G>A Likely pathogenic ★★ same type
- DNAAF4 p.Arg245Ter Pathogenic/Likely pathogenic ★★ same type
- DNAAF4 p.Arg270Ter Pathogenic/Likely pathogenic ★★ same type
- DNAAF4 p.Arg330Trp Pathogenic/Likely pathogenic ★★ same type
- DNAAF4 p.Arg371Ter Pathogenic/Likely pathogenic ★★ 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/dnaaf4-p-thr303 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown