Is PHIP p.Val975= (c.2925C>A) pathogenic?

PHIP p.Val975= (c.2925C>A) is classified Likely benign in PHIP (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-09-08). Ultra-rare (popmax 0.0222%, nfe).

How common is PHIP p.Val975= (c.2925C>A) in the general population?

PHIP p.Val975= (c.2925C>A) is ultra-rare (popmax 0.0222%, nfe) (gnomAD).

PHIP p.Val975=

c.2925C>A · rs140757402 · VCV1299038

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0222%, nfe)

⚠ 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 3	GERP -5.9, phastCons 1
Overall
CADD	1.027	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0222% European (non-Finnish) · 262/1,178,388 alleles

Filtering AF 0.02% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0192%

Overall 0.0173% 279/1,610,248 alleles · ultra-rare exomes 246/1,458,324 · genomes 33/151,924 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.0222%	4,498
Remaining individualsnot grpmax-eligible	0.0112%	8,907
Finnishnot grpmax-eligible	0.011%	9,124
African / African-American	0.00268%	37,303
South Asian	0.00111%	90,248

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.Val975=
Coding: c.2925C>A
MANE Select: NM_017934
dbSNP: rs140757402
Type: single nucleotide variant
Location: chr6:78970853 (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-val975 (accessed [today's date]).

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