PHF6 p.Asp309=
c.927C>T · rs112199174 · VCV129887
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 7 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.64%, afr)
Conditions
2
Inborn genetic diseases
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 1.8 | GERP 1.3, phastCons 1 |
| Overall | ||
| CADD | 9.841 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.64%
African / African-American · 1,513/57,226 alleles
Filtering AF
2.53%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.49%
Overall
0.146%
1,765/1,208,241 alleles · low-frequency
exomes 933/1,096,140 · genomes 832/112,101 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.64% | 38 |
| Middle Eastern | 0.322% | 311 |
| Remaining individualsnot grpmax-eligible | 0.29% | 344 |
| Admixed American | 0.155% | 645 |
| South Asian | 0.00352% | 28,392 |
| European (non-Finnish) | 0.00313% | 31,926 |
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
- PHF6
- Protein
- p.Asp309=
- Coding
- c.927C>T
- MANE Select
- NM_001015877
- dbSNP
- rs112199174
- Type
- single nucleotide variant
- Location
- chrX:134417261 (GRCh38)
- Structure
- AlphaFold pLDDT 73.45 · 2 PDB
- Residue 309
- the 'extended phd2 domain (ephd2)' region
Similar variants
- PHF6 p.Arg116Ter Pathogenic ★★ same condition
- PHF6 p.Arg225Ter Pathogenic ★★ same condition
- PHF6 p.Arg274Ter Pathogenic ★★ same condition
- PHF6 p.Arg342Ter Pathogenic ★★ same condition
- PHF6 p.Cys45Tyr Pathogenic ★★ same condition
- PHF6 p.Met1Thr Pathogenic ★★ same condition
- PHF6 p.Arg163His Uncertain significance ★★ ⚠ same condition
- PHF6 p.Arg166Lys Uncertain significance ★★ ⚠ same condition
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/phf6-p-asp309 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown