IPP p.Thr179=
c.537G>A · VCV4679279
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00754%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.57 | GERP 0.41, phastCons 0.072 |
| Overall | ||
| CADD | 9.051 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00754%
European (non-Finnish) · 89/1,179,982 alleles
Filtering AF
0.00623%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00579%
Overall
0.00576%
93/1,614,084 alleles · very rare
exomes 89/1,461,798 · genomes 4/152,286 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00754% | 13,258 |
| African / African-American | 0.00267% | 37,523 |
| Admixed American | 0.00167% | 60,016 |
| South Asian | 0.0011% | 91,080 |
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
- IPP
- Protein
- p.Thr179=
- Coding
- c.537G>A
- MANE Select
- NM_005897
- Type
- single nucleotide variant
- Location
- chr1:45741088 (GRCh38)
- Gene constraint
- LOEUF 0.956 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 90.12
Similar variants
- IPP p.Ala203Gly Uncertain significance ★ ⚠ same type
- IPP p.Ala204Val Uncertain significance ★ same type
- IPP p.Ala374Val Uncertain significance ★ ⚠ same type
- IPP p.Ala476Val Uncertain significance ★ ⚠ same type
- IPP p.Ala524Val Uncertain significance ★ same type
- IPP p.Ala57Ser Uncertain significance ★ ⚠ same type
- IPP p.Arg283Trp Uncertain significance ★ ⚠ same type
- IPP p.Arg298Gln Uncertain significance ★ ⚠ 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/ipp-p-thr179 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown