HAND1 p.Ala71=
c.213C>A · VCV4972772
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000944%)
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 1.2 | GERP -3.2, phastCons 1 |
| Overall | ||
| CADD | 10.03 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000944%
Overall
0.000944%
15/1,589,576 alleles · very rare
exomes 12/1,437,454 · genomes 3/152,122 · 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
- HAND1
- Protein
- p.Ala71=
- Coding
- c.213C>A
- MANE Select
- NM_004821
- Type
- single nucleotide variant
- Location
- chr5:154477796 (GRCh38)
- Gene constraint
- LOEUF 1.188 · pLI 0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 65.87
- Residue 71
- the 'disordered' region
Similar variants
- HAND1 p.Ala68Pro Uncertain significance ★★ ⚠ same type
- HAND1 p.Arg91Gly Uncertain significance ★★ ⚠ same type
- HAND1 p.Gln43Arg Uncertain significance ★★ ⚠ same type
- HAND1 p.Glu103Gly Uncertain significance ★★ ⚠ same type
- HAND1 p.Gly203Ala Uncertain significance ★★ ⚠ same type
- HAND1 p.Leu3Val Uncertain significance ★★ ⚠ same type
- HAND1 p.Pro125Arg Uncertain significance ★★ ⚠ same type
- HAND1 p.Pro188Ala 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/hand1-p-ala71 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown