PHF8 p.Ile248=
c.744T>C · rs2519674575 · VCV1758976
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
Inborn genetic diseases
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.102 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 4.8 | phastCons 1 |
| Overall | ||
| CADD | 9.648 | 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
- PHF8
- Protein
- p.Ile248=
- Coding
- c.744T>C
- MANE Select
- NM_015107
- dbSNP
- rs2519674575
- Type
- single nucleotide variant
- Location
- chrX:54014416 (GRCh38)
- Structure
- AlphaFold pLDDT 63.30 · 6 PDB
- Residue 248
- the jmjc domain; an α-helix
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-ile248 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown