DNAAF4 p.Thr85=
c.255C>A · rs1303568671 · VCV2174366
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00017%, nfe)
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 0.097 | GERP -4.2, phastCons 0.006 |
| Overall | ||
| CADD | 3.858 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00017%
European (non-Finnish) · 2/1,179,014 alleles
Filtering AF
2.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.1e-05%
Overall
0.000124%
2/1,610,934 alleles · very rare
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.Thr85=
- Coding
- c.255C>A
- MANE Select
- NM_130810
- dbSNP
- rs1303568671
- Type
- single nucleotide variant
- Location
- chr15:55497728 (GRCh38)
- Gene constraint
- LOEUF 1.018 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 84.00
- Residue 85
- the cs domain; the 'mediates interaction with esr1 and stub1' region
Similar variants
- 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
- DNAAF4 p.Gln4Ter 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-thr85 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown