Sugi Variant
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PHIP/p.Arg1220=

PHIP p.Arg1220=

c.3660G>A · rs2481849142 · VCV2656716

Likely benign Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 6.42e-05%)

⚠ 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
ConservationphyloP -5.3GERP -5.7
Overall
CADD1.599PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes
Grpmax group 6.42e-05%
Overall 6.42e-05% 1/1,558,060 alleles · very rare exomes 1/1,406,224 · genomes 0/151,836 · 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.Arg1220=
Coding
c.3660G>A
MANE Select
NM_017934
dbSNP
rs2481849142
Type
single nucleotide variant
Location
chr6:78958597 (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-arg1220 (accessed [today's date]).

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