Is PHIP p.Arg1402Ser (c.4206G>T) pathogenic?

PHIP p.Arg1402Ser (c.4206G>T) is classified Likely pathogenic in PHIP (ClinVar, Single submitter, 1 submitter; last evaluated 2017-06-05). AlphaMissense: likely pathogenic (0.988); No allele count reported in gnomAD v4.1 (AN 1,364,624).

How common is PHIP p.Arg1402Ser (c.4206G>T) in the general population?

PHIP p.Arg1402Ser (c.4206G>T) is no allele count reported in gnomAD v4.1 (AN 1,364,624) (gnomAD).

What do computational predictors say about PHIP p.Arg1402Ser (c.4206G>T)?

AlphaMissense predicts likely pathogenic (score 0.988) — an in-silico prediction, not a clinical call.

PHIP p.Arg1402Ser

c.4206G>T · rs1363133370 · VCV432452

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.988 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,364,624)

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

⚠ Built without this gene's context — gene constraint and dosage, protein structure, pathways, panels and related-variant links were not looked up for this page. why

Computational evidence

Protein change
AlphaMissense	0.988	likely pathogenic ✓ concordant with ClinVar
REVEL	0.102	moderately benign-leaning
SaProt	LLR -5.19	tolerated
⇒ AlphaMissense calls this damaging; REVEL and SaProt do not.
Splicing
SpliceAI	—	not looked up on this page · why
Pangolin	Δ0.67	loss · gain 0.06 · independent
Constraint at this position
Conservation	phyloP 7.7	GERP 2.9, phastCons 1
Regional constraint	o/e 0.53	unconstrained · MANE · 9,095 bp · p 7e-13 · regional, not allelic
Overall
CADD	35.0	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,364,624). 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.Arg1402Ser
Coding: c.4206G>T
MANE Select: NM_017934
dbSNP: rs1363133370
Type: single nucleotide variant
Location: chr6:78947623 (GRCh38)

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

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-arg1402ser (accessed [today's date]).

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