PHF6 p.Thr255=
c.765A>T · rs2520636060 · VCV3026841
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
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 2.9 | GERP -3.7, phastCons 1 |
| Overall | ||
| CADD | 7.131 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- PHF6
- Protein
- p.Thr255=
- Coding
- c.765A>T
- MANE Select
- NM_001015877
- dbSNP
- rs2520636060
- Type
- single nucleotide variant
- Location
- chrX:134415051 (GRCh38)
- Structure
- AlphaFold pLDDT 73.45 · 2 PDB
- Residue 255
- the 'extended phd2 domain (ephd2)' region
Similar variants
- PHF6 p.Thr255del Uncertain significance ★★ same residue
- PHF6 p.Arg116Ter Pathogenic ★★ same type
- PHF6 p.Arg225Ter Pathogenic ★★ same type
- PHF6 p.Arg274Ter Pathogenic ★★ same type
- PHF6 p.Arg342Ter Pathogenic ★★ same type
- PHF6 p.Cys45Tyr Pathogenic ★★ same type
- PHF6 p.Met1Thr Pathogenic ★★ same type
- PHF6 p.Arg163His 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/phf6-p-thr255 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown