Is PHIP p.Ser287fs (c.857dup) pathogenic?

PHIP p.Ser287fs (c.857dup) is classified Pathogenic in PHIP (ClinVar, Single submitter, 1 submitter; last evaluated 2024-09-01). No gnomAD frequency available for this variant.

How common is PHIP p.Ser287fs (c.857dup) in the general population?

PHIP p.Ser287fs (c.857dup) is no gnomAD frequency available for this variant (gnomAD).

PHIP p.Ser287fs

c.857dup · rs2482185944 · VCV3239498

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

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 9 of 40
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -10	GERP -3.7

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.Ser287fs
Coding: c.857dup
MANE Select: NM_017934
dbSNP: rs2482185944
Type: Duplication
Location: chr6:79025584 (GRCh38)
Gene constraint: LOEUF 0.246 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 66.57 · 146 PDB
Residue 287: a UniProt-annotated variant site (in chujans)

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

Similar variants

PHIP p.Ser287Tyr Likely pathogenic ★★ ⚠ same residue
PHIP p.Ala124fs Pathogenic ★ same type
PHIP p.Cys520fs Likely pathogenic ★ same type
PHIP p.Gly351fs Pathogenic ★ same type
PHIP p.Ile440fs Pathogenic ★ same type
PHIP p.Met508fs Likely pathogenic ★ same type
PHIP p.Pro144fs Likely pathogenic ★ same type
PHIP p.Thr750fs Pathogenic ★ same type

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-ser287fs (accessed [today's date]).

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