HOXA2 p.Pro84=
c.252G>C · VCV4895521
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000179%, 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 -0.92 | GERP -6.7, phastCons 0.004 |
| Overall | ||
| CADD | 9.273 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000179%
European (non-Finnish) · 2/1,115,078 alleles
Filtering AF
3e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.1e-05%
Overall
0.000135%
2/1,477,624 alleles · very rare
exomes 2/1,325,626 · genomes 0/151,998 · 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
- HOXA2
- Protein
- p.Pro84=
- Coding
- c.252G>C
- MANE Select
- NM_006735
- Type
- single nucleotide variant
- Location
- chr7:27102249 (GRCh38)
- Gene constraint
- LOEUF 0.334 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 58.47
- Residue 84
- the 'disordered' region
Similar variants
- HOXA2 p.Pro84Arg Uncertain significance ★ ⚠ same residue
- HOXA2 p.Pro84fs Likely pathogenic ★ same residue
- HOXA2 p.Asp324Asn Uncertain significance ★★ ⚠ same type
- HOXA2 p.Leu336Val Uncertain significance ★★ ⚠ same type
- HOXA2 p.Pro27Arg Uncertain significance ★★ ⚠ same type
- HOXA2 p.Ser132Thr Uncertain significance ★★ ⚠ same type
- HOXA2 p.Ser269= Uncertain significance ★★ same type
- HOXA2 p.Ser269Phe 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/hoxa2-p-pro84 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown