Is PHIP p.Lys891fs (c.2670_2671del) pathogenic?

PHIP p.Lys891fs (c.26702671del) is classified Pathogenic in PHIP (ClinVar, Single submitter, 1 submitter; last evaluated 2023-09-12). No gnomAD frequency available for this variant; Associated with PHIP-related disorder.

What condition is associated with PHIP p.Lys891fs (c.2670_2671del)?

PHIP p.Lys891fs (c.2670_2671del) is associated with PHIP-related disorder (ClinVar).

How common is PHIP p.Lys891fs (c.2670_2671del) in the general population?

PHIP p.Lys891fs (c.2670_2671del) is no gnomAD frequency available for this variant (gnomAD).

PHIP p.Lys891fs

c.2670_2671del · rs2481963256 · VCV2630755

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

PHIP-related disorder

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 23 of 40
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 7.9	GERP -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: PHIP
Protein: p.Lys891fs
Coding: c.2670_2671del
MANE Select: NM_017934
dbSNP: rs2481963256
Type: Deletion
Location: chr6:78982984 (GRCh38)
Gene constraint: LOEUF 0.246 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 66.57 · 146 PDB
Residue 891: the 'disordered' region; a UniProt-annotated variant site (in chujans)

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

Disease context

PHIP-related disorder

Similar variants

PHIP p.Ile307fs Pathogenic/Likely pathogenic ★★ same condition
PHIP p.Glu904fs Likely pathogenic ★ same condition
PHIP p.Tyr348fs Likely pathogenic ★ same condition
PHIP p.Val771Ile Uncertain significance ★★ ⚠ same condition
PHIP c.1096-2A>C Likely pathogenic ★ same condition
PHIP c.822+1G>A Likely pathogenic ★ same condition
PHIP p.Glu55Ter Likely pathogenic ★ same condition
PHIP p.Glu755Ter Likely 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/phip-p-lys891fs (accessed [today's date]).

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