PHF8 p.Val977=
c.2931C>T · rs1315181495 · VCV1797821
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0209%, amr)
Conditions
1
Inborn genetic diseases
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.026 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
| Constraint at this position | ||
| Conservation | phyloP 2.1 | GERP -1.6, phastCons 1 |
| Overall | ||
| CADD | 5.911 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0209%
Admixed American · 9/42,984 alleles
Filtering AF
0.0109%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00809%
Overall
0.000755%
9/1,192,477 alleles · ultra-rare
exomes 6/1,080,380 · genomes 3/112,097 · 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.Val977=
- Coding
- c.2931C>T
- MANE Select
- NM_015107
- dbSNP
- rs1315181495
- Type
- single nucleotide variant
- Location
- chrX:53940235 (GRCh38)
- Structure
- AlphaFold pLDDT 63.30 · 6 PDB
- Residue 977
- the 'disordered' region
Similar variants
- PHF8 p.Arg506Ter Pathogenic/Likely pathogenic ★★ same condition
- PHF8 p.Ala770Pro Uncertain significance ★★ ⚠ same condition
- PHF8 p.Arg240Gln Uncertain significance ★★ ⚠ same condition
- PHF8 p.Arg438His Uncertain significance ★★ same condition
- PHF8 p.Arg588Gln Uncertain significance ★★ ⚠ same condition
- PHF8 p.Arg773Pro Uncertain significance ★★ ⚠ same condition
- PHF8 p.Arg968Cys Uncertain significance ★★ ⚠ same condition
- PHF8 p.Arg982Trp 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/phf8-p-val977 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown