PHIP p.Arg752=
c.2256G>A · rs149171291 · VCV1336139
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 5 submitters
gnomAD v4.1
Rare
rare (popmax 0.673%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.38 | GERP -0.94, phastCons 0.11 |
| Overall | ||
| CADD | 5.316 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.673%
African / African-American · 504/74,944 alleles
Filtering AF
0.624%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.605%
Overall
0.0407%
656/1,611,846 alleles · rare
exomes 342/1,459,644 · genomes 314/152,202 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.673% | 149 |
| Ashkenazi Jewishnot grpmax-eligible | 0.156% | 643 |
| Remaining individualsnot grpmax-eligible | 0.0625% | 1,600 |
| Middle Eastern | 0.0496% | 2,017 |
| Admixed American | 0.0434% | 2,303 |
| European (non-Finnish) | 0.00314% | 31,851 |
| South Asian | 0.0011% | 90,892 |
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.Arg752=
- Coding
- c.2256G>A
- MANE Select
- NM_017934
- dbSNP
- rs149171291
- Type
- single nucleotide variant
- Location
- chr6:78990931 (GRCh38)
- Gene constraint
- LOEUF 0.246 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 66.57 · 146 PDB
- Residue 752
- the 'disordered' region; a UniProt-annotated variant site (in chujans)
Similar variants
- PHIP p.Arg752Gly Likely benign ★ same residue
- PHIP p.Arg110Cys Pathogenic/Likely pathogenic ★★ same type
- PHIP p.Arg178Ter Pathogenic/Likely pathogenic ★★ same type
- PHIP p.Arg193Ter Pathogenic ★★ same type
- PHIP p.Arg255Ter Pathogenic/Likely pathogenic ★★ same type
- PHIP p.Arg396Ter Pathogenic/Likely pathogenic ★★ same type
- PHIP p.Arg503Ter Pathogenic/Likely pathogenic ★★ same type
- PHIP p.Arg721Ter Pathogenic/Likely pathogenic ★★ same type
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-arg752 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown