PHF8 p.Arg211Ter
c.631C>T · rs121918522 · VCV10798
Pathogenic
No assertion criteria
Classification
Pathogenic
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
Consequence
nonsense (stop-gain)
predicted LoF
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
syndromic X-linked intellectual disability Siderius type
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | nonsense (stop-gain) | predicted loss-of-function in a haploinsufficient gene (ClinGen) |
|---|---|---|
| NMD | predicted | premature termination codon in exon 7 of 22 |
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
| Pangolin | Δ0.36 | loss · gain 0.00 · SpliceAI below 0.2 · independent |
| Constraint at this position | ||
| Conservation | phyloP 5.9 | phastCons 1 |
| Overall | ||
| CADD | 37.0 | PHRED · no single calibrated threshold — expert panels disagree |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
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.Arg211Ter
- Coding
- c.631C>T
- MANE Select
- NM_015107
- dbSNP
- rs121918522
- Type
- single nucleotide variant
- Location
- chrX:54014529 (GRCh38)
- Structure
- AlphaFold pLDDT 63.30 · 6 PDB
- Residue 211
- an α-helix
Similar variants
- PHF8 p.Arg240Ter Likely pathogenic ★★ same condition
- PHF8 p.Arg506Ter Pathogenic/Likely pathogenic ★★ same condition
- PHF8 p.Arg753Ter Pathogenic/Likely pathogenic ★★ same condition
- PHF8 p.Arg66His Uncertain significance ★★ ⚠ same condition
- PHF8 p.Arg753Gln Uncertain significance ★★ ⚠ same condition
- PHF8 p.Arg773Pro Uncertain significance ★★ ⚠ same condition
- PHF8 p.Leu949Phe Uncertain significance ★★ ⚠ same condition
- PHF8 p.Tyr706Cys 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-arg211ter (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown