MEIS2 p.Pro30=
c.90G>T · VCV4924131
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00186%, 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 0.82 | GERP -2, phastCons 1 |
| Overall | ||
| CADD | 13.54 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00186%
European (non-Finnish) · 22/1,179,830 alleles
Filtering AF
0.00122%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00104%
Overall
0.00143%
23/1,613,254 alleles · very rare
exomes 22/1,461,380 · genomes 1/151,874 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00186% | 53,629 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,462 |
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
- MEIS2
- Protein
- p.Pro30=
- Coding
- c.90G>T
- MANE Select
- NM_170675
- Type
- single nucleotide variant
- Location
- chr15:37098122 (GRCh38)
- Gene constraint
- LOEUF 0.255 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 63.16 · 4 PDB
Similar variants
- MEIS2 p.Arg174Ter Pathogenic ★★ same type
- MEIS2 p.Arg219Ter Pathogenic/Likely pathogenic ★★ same type
- MEIS2 p.Asp169Asn Uncertain significance ★★ ⚠ same type
- MEIS2 p.Asp6Ala Uncertain significance ★★ ⚠ same type
- MEIS2 p.His447Gln Uncertain significance ★★ ⚠ same type
- MEIS2 p.Ile33Val Uncertain significance ★★ ⚠ same type
- MEIS2 p.Leu154Ile Uncertain significance ★★ ⚠ same type
- MEIS2 p.Pro416Arg 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/meis2-p-pro30 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown