MEIS2 p.Ala2=
c.6G>A · rs1329697250 · VCV1933828
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 6.2e-05%)
Conditions
1
cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies
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 5.7 | GERP 0.56, phastCons 1 |
| Overall | ||
| CADD | 16.09 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
6.2e-05%
Overall
6.2e-05%
1/1,613,932 alleles · very rare
exomes 1/1,461,844 · genomes 0/152,088 · joint denominator
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.Ala2=
- Coding
- c.6G>A
- MANE Select
- NM_170675
- dbSNP
- rs1329697250
- Type
- single nucleotide variant
- Location
- chr15:37099461 (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 condition
- MEIS2 p.Arg219Ter Pathogenic/Likely pathogenic ★★ same condition
- MEIS2 p.Asp169Asn Uncertain significance ★★ ⚠ same condition
- MEIS2 p.Asp6Ala Uncertain significance ★★ ⚠ same condition
- MEIS2 p.Ile33Val Uncertain significance ★★ ⚠ same condition
- MEIS2 p.Pro416Arg Uncertain significance ★★ ⚠ same condition
- MEIS2 c.13-19C>A Benign/Likely benign ★★ same condition
- MEIS2 c.754+7G>C Likely benign ★★ same condition
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-ala2 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown