PHF6 p.Ile290=
c.870T>C · rs763116203 · VCV2722367
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00369%, nfe)
Conditions
1
Borjeson-Forssman-Lehmann syndrome
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 2.3 | GERP 0.48, phastCons 1 |
| Overall | ||
| CADD | 9.586 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00369%
European (non-Finnish) · 33/893,997 alleles
Filtering AF
0.00263%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00232%
Overall
0.00281%
34/1,208,976 alleles · very rare
exomes 31/1,096,447 · genomes 3/112,529 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00369% | 27,091 |
| African / African-American | 0.00174% | 57,379 |
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
- PHF6
- Protein
- p.Ile290=
- Coding
- c.870T>C
- MANE Select
- NM_001015877
- dbSNP
- rs763116203
- Type
- single nucleotide variant
- Location
- chrX:134417204 (GRCh38)
- Structure
- AlphaFold pLDDT 73.45 · 2 PDB
- Residue 290
- a β-strand; the 'extended phd2 domain (ephd2)' region
Similar variants
- PHF6 p.Arg116Ter Pathogenic ★★ same condition
- PHF6 p.Arg225Ter Pathogenic ★★ same condition
- PHF6 p.Arg274Ter Pathogenic ★★ same condition
- PHF6 p.Arg342Ter Pathogenic ★★ same condition
- PHF6 p.Cys45Tyr Pathogenic ★★ same condition
- PHF6 p.Met1Thr Pathogenic ★★ same condition
- PHF6 p.Arg163His Uncertain significance ★★ ⚠ same condition
- PHF6 p.Arg166Lys 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/phf6-p-ile290 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown