Is PHIP p.Asp1047= (c.3141C>T) pathogenic?

PHIP p.Asp1047= (c.3141C>T) is classified Likely benign in PHIP (ClinVar, Single submitter, 1 submitter; last evaluated 2025-04-07). Ultra-rare (popmax 0.0445%, sas).

How common is PHIP p.Asp1047= (c.3141C>T) in the general population?

PHIP p.Asp1047= (c.3141C>T) is ultra-rare (popmax 0.0445%, sas) (gnomAD).

PHIP p.Asp1047=

c.3141C>T · rs577361790 · VCV2778724

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0445%, sas)

⚠ 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 -0.41	GERP -5.9
Overall
CADD	8.57	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0445% South Asian · 40/89,906 alleles

Filtering AF 0.0335% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0297%

Overall 0.00313% 50/1,599,186 alleles · ultra-rare exomes 47/1,447,028 · genomes 3/152,158 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0445%	2,248
Remaining individualsnot grpmax-eligible	0.00323%	30,965
East Asian	0.00224%	44,668
African / African-American	0.00134%	74,612
European (non-Finnish)	0.000513%	194,794

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.Asp1047=
Coding: c.3141C>T
MANE Select: NM_017934
dbSNP: rs577361790
Type: single nucleotide variant
Location: chr6:78969899 (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-asp1047 (accessed [today's date]).

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