PHF8 p.Ser933=
c.2799A>T · VCV4951006
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0124%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.018 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
| Constraint at this position | ||
| Conservation | phyloP -4.2 | GERP 0.006 |
| Overall | ||
| CADD | 1.195 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0124%
South Asian · 7/56,333 alleles
Filtering AF
0.00575%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00411%
Overall
0.00058%
7/1,207,312 alleles · ultra-rare
exomes 6/1,096,309 · genomes 1/111,003 · joint denominator
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
- PHF8
- Protein
- p.Ser933=
- Coding
- c.2799A>T
- MANE Select
- NM_015107
- Type
- single nucleotide variant
- Location
- chrX:53940367 (GRCh38)
- Structure
- AlphaFold pLDDT 63.30 · 6 PDB
- Residue 933
- the 'disordered' region
Similar variants
- PHF8 p.Ser933del Benign/Likely benign ★★ same residue
- PHF8 p.Arg240Ter Likely pathogenic ★★ same type
- PHF8 p.Arg506Ter Pathogenic/Likely pathogenic ★★ same type
- PHF8 p.Arg753Ter Pathogenic/Likely pathogenic ★★ same type
- PHF8 p.Gln539Ter Pathogenic ★★ same type
- PHF8 p.Ser737Ter Pathogenic/Likely pathogenic ★★ same type
- PHF8 p.Ala770Pro Uncertain significance ★★ ⚠ same type
- PHF8 p.Ala888Ser 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/phf8-p-ser933 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown