Is PHIP p.Phe1413= (c.4239C>T) pathogenic?

PHIP p.Phe1413= (c.4239C>T) is classified Likely benign in PHIP (ClinVar, Single submitter, 2 submitters; last evaluated 2025-03-19). Ultra-rare (popmax 0.0195%, amr).

How common is PHIP p.Phe1413= (c.4239C>T) in the general population?

PHIP p.Phe1413= (c.4239C>T) is ultra-rare (popmax 0.0195%, amr) (gnomAD).

PHIP p.Phe1413=

c.4239C>T · rs766384766 · VCV2160807

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0195%, amr)

⚠ 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
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 5.1	GERP 2, phastCons 1
Overall
CADD	8.604	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0195% Admixed American · 10/51,174 alleles

Filtering AF 0.0105% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00806%

Overall 0.00076% 12/1,578,006 alleles · ultra-rare exomes 12/1,426,502 · genomes 0/151,504 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.0195%	5,117
East Asian	0.00232%	43,036
European (non-Finnish)	8.57e-05%	1,166,583

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: PHIP
Protein: p.Phe1413=
Coding: c.4239C>T
MANE Select: NM_017934
dbSNP: rs766384766
Type: single nucleotide variant
Location: chr6:78946842 (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-phe1413 (accessed [today's date]).

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