PHIP p.Leu286=
c.858A>G · rs201059253 · VCV2184310
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00769%, sas)
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 -10 | GERP -3.7 |
| Overall | ||
| CADD | 0.591 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00769%
South Asian · 7/91,028 alleles
Filtering AF
0.00367%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0033%
Overall
0.00434%
70/1,611,750 alleles · very rare
exomes 61/1,459,564 · genomes 9/152,186 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00769% | 13,004 |
| Remaining individualsnot grpmax-eligible | 0.00481% | 20,801 |
| European (non-Finnish) | 0.00467% | 21,418 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,582 |
| Admixed American | 0.00333% | 29,992 |
| African / African-American | 0.00267% | 37,444 |
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.Leu286=
- Coding
- c.858A>G
- MANE Select
- NM_017934
- dbSNP
- rs201059253
- Type
- single nucleotide variant
- Location
- chr6:79025584 (GRCh38)
- Gene constraint
- LOEUF 0.246 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 66.57 · 146 PDB
- Residue 286
- a UniProt-annotated variant site (in chujans)
Similar variants
- 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
- PHIP p.Asn507Ser 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-leu286 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown