Is PHF6 p.Pro11fs (c.29_30dup) pathogenic?

PHF6 p.Pro11fs (c.2930dup) is classified Pathogenic in PHF6 (ClinVar, Single submitter, 1 submitter; last evaluated 2017-12-09). No gnomAD frequency available for this variant; Associated with Borjeson-Forssman-Lehmann syndrome.

What condition is associated with PHF6 p.Pro11fs (c.29_30dup)?

PHF6 p.Pro11fs (c.29_30dup) is associated with Borjeson-Forssman-Lehmann syndrome (ClinVar).

How common is PHF6 p.Pro11fs (c.29_30dup) in the general population?

PHF6 p.Pro11fs (c.29_30dup) is no gnomAD frequency available for this variant (gnomAD).

PHF6 p.Pro11fs

c.29_30dup · rs1556013203 · VCV488575

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

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 2 of 11
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 1.9	GERP -4.2, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: PHF6
Protein: p.Pro11fs
Coding: c.29_30dup
MANE Select: NM_001015877
dbSNP: rs1556013203
Type: Duplication
Location: chrX:134377644 (GRCh38)
Structure: AlphaFold pLDDT 73.45 · 2 PDB

Full PHF6 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Borjeson-Forssman-Lehmann syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

PHF6 p.Pro11Ser Uncertain significance ★★ ⚠ same residue
PHF6 p.Ser61fs 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

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-pro11fs (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown