PHIP p.Asn490=
c.1470C>T · rs375350790 · VCV2140835
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0329%, mid)
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 -0.74 | GERP -4 |
| Overall | ||
| CADD | 4.242 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0329%
Middle Eastern · 2/6,072 alleles
Filtering AF
0.00581%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00242%
Overall
0.00118%
19/1,610,858 alleles · ultra-rare
exomes 17/1,459,210 · genomes 2/151,648 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0329% | 3,036 |
| South Asian | 0.0044% | 22,747 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,372 |
| African / African-American | 0.00134% | 74,770 |
| European (non-Finnish) | 0.000934% | 107,055 |
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.Asn490=
- Coding
- c.1470C>T
- MANE Select
- NM_017934
- dbSNP
- rs375350790
- Type
- single nucleotide variant
- Location
- chr6:79015136 (GRCh38)
- Gene constraint
- LOEUF 0.246 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 66.57 · 146 PDB
- Residue 490
- 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-asn490 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown