IPMK p.Thr32=
c.96C>G · rs61740967 · VCV720679
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.45%, afr)
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 1.4 | GERP 0.44, phastCons 0.98 |
| Overall | ||
| CADD | 9.923 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.45%
African / African-American · 1,091/75,060 alleles
Filtering AF
1.38%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.35%
Overall
0.0962%
1,552/1,613,310 alleles · low-frequency
exomes 869/1,460,972 · genomes 683/152,338 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.45% | 69 |
| Middle Eastern | 0.233% | 430 |
| Remaining individualsnot grpmax-eligible | 0.16% | 624 |
| Admixed American | 0.127% | 789 |
| European (non-Finnish) | 0.0216% | 4,627 |
| South Asian | 0.0165% | 6,070 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,572 |
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
- IPMK
- Protein
- p.Thr32=
- Coding
- c.96C>G
- MANE Select
- NM_152230
- dbSNP
- rs61740967
- Type
- single nucleotide variant
- Location
- chr10:58267516 (GRCh38)
- Gene constraint
- LOEUF 0.6 · pLI 0.82 (gnomAD)
- Structure
- AlphaFold pLDDT 74.50 · 25 PDB
- Residue 32
- the 'disordered' region
Similar variants
- IPMK p.Thr32Asn Uncertain significance ★ ⚠ same residue
- IPMK p.Asn124= Benign ★★ same type
- IPMK p.Ala228Val Uncertain significance ★ ⚠ same type
- IPMK p.Ala250Thr Uncertain significance ★ ⚠ same type
- IPMK p.Ala319Val Uncertain significance ★ ⚠ same type
- IPMK p.Arg10Gln Uncertain significance ★ ⚠ same type
- IPMK p.Arg10Trp Uncertain significance ★ ⚠ same type
- IPMK p.Arg320His 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/ipmk-p-thr32 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown