PHF6 p.Ser61fs
c.181dup · VCV4795937
Pathogenic
Single submitter
Classification
Pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Conditions
1
Borjeson-Forssman-Lehmann syndrome
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function in a haploinsufficient gene (ClinGen) |
|---|---|---|
| NMD | predicted | premature termination codon in exon 3 of 11 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 9.9 | GERP 2, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- PHF6
- Protein
- p.Ser61fs
- Coding
- c.181dup
- MANE Select
- NM_001015877
- Type
- Duplication
- Location
- chrX:134378044 (GRCh38)
- Structure
- AlphaFold pLDDT 73.45 · 2 PDB
- Residue 61
- the 'extended phd1 domain (ephd1)' region
Similar variants
- PHF6 p.Pro11fs Pathogenic ★ same condition
- PHF6 p.Glu343fs Uncertain significance ★ same condition
- PHF6 c.374+21dup Likely benign ★ same condition
- PHF6 c.585+14dup Benign ★ same condition
- PHF6 p.Gly10fs Pathogenic same condition
- PHF6 p.Arg116Ter Pathogenic ★★ same condition
- PHF6 p.Arg225Ter Pathogenic ★★ same condition
- PHF6 p.Arg274Ter Pathogenic ★★ 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-ser61fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown