Is PHIP p.Leu930= (c.2790A>G) pathogenic?

PHIP p.Leu930= (c.2790A>G) is classified Likely benign in PHIP (ClinVar, Single submitter, 2 submitters; last evaluated 2022-06-26). Very rare (popmax 0.000342%, nfe).

How common is PHIP p.Leu930= (c.2790A>G) in the general population?

PHIP p.Leu930= (c.2790A>G) is very rare (popmax 0.000342%, nfe) (gnomAD).

PHIP p.Leu930=

c.2790A>G · rs1488931812 · VCV2010800

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 0.000342%, 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 -0.006	GERP -5.5, phastCons 0.9
Overall
CADD	4.718	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.000342% European (non-Finnish) · 4/1,169,278 alleles

Filtering AF 8e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 5.4e-05%

Overall 0.00025% 4/1,598,910 alleles · very rare exomes 4/1,446,642 · genomes 0/152,268 · joint denominator

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.Leu930=
Coding: c.2790A>G
MANE Select: NM_017934
dbSNP: rs1488931812
Type: single nucleotide variant
Location: chr6:78978691 (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-leu930 (accessed [today's date]).

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