PHIP p.Asp1060=

Q: Is PHIP p.Asp1060= (c.3180T>C) pathogenic?

PHIP p.Asp1060= (c.3180T>C) is classified Benign in PHIP (ClinVar, Multiple submitters, 4 submitters; last evaluated 2026-02-03). Common (popmax 67.7%, eas) — too common for a highly-penetrant pathogenic allele; Associated with PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome.

Q: What condition is associated with PHIP p.Asp1060= (c.3180T>C)?

PHIP p.Asp1060= (c.3180T>C) is associated with PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome (ClinVar).

Q: How common is PHIP p.Asp1060= (c.3180T>C) in the general population?

PHIP p.Asp1060= (c.3180T>C) is common (popmax 67.7%, eas) — too common for a highly-penetrant pathogenic allele (gnomAD).

Q: How is PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome inherited?

Typically Autosomal dominant (Orphanet). A genetic counselor can assess individual risk for a family.

c.3180T>C · rs7742431 · VCV1226668

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

gnomAD v4.1

Common

common (popmax 67.7%, eas) — too common for a highly-penetrant pathogenic allele

Conditions

PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome

⚠ 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 -1.7	GERP -5.9
Overall
CADD	0.532	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 67.7% East Asian · 30,117/44,518 alleles

Filtering AF 67% ClinGen BA1/BS1 input FAF95, joint · FAF99 66.7%

Overall 50.7% 799,136/1,575,178 alleles · common exomes 724,736/1,423,178 · genomes 74,400/152,000 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	67.7%	1
South Asian	64.1%	2
Ashkenazi Jewishnot grpmax-eligible	51.6%	2
Remaining individualsnot grpmax-eligible	50.9%	2
Amishnot grpmax-eligible	50.8%	2
European (non-Finnish)	49.9%	2
Finnishnot grpmax-eligible	48.2%	2
Middle Eastern	47%	2
Admixed American	46.2%	2
African / African-American	42.7%	2

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.Asp1060=
Coding: c.3180T>C
MANE Select: NM_017934
dbSNP: rs7742431
Type: single nucleotide variant
Location: chr6:78969860 (GRCh38)

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

Disease context

For PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome (Orphanet):

Inheritance: Autosomal dominant
Onset: Antenatal, Infancy, Neonatal

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-asp1060 (accessed [today's date]).

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