HAND2 p.Pro90fs
c.269_320del · VCV3661904
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function |
|---|---|---|
| NMD | predicted | premature termination codon in exon 1 of 2 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 1.7 | GERP -2, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- HAND2
- Protein
- p.Pro90fs
- Coding
- c.269_320del
- MANE Select
- NM_021973
- Type
- Deletion
- Location
- chr4:173528970 (GRCh38)
- Gene constraint
- LOEUF 0.601 · pLI 0.89 (gnomAD)
- Structure
- AlphaFold pLDDT 67.30
- Residue 90
- the 'disordered' region
Similar variants
- HAND2 p.Pro90Arg Conflicting classifications of pathogenicity ★ ⚠ same residue
- HAND2 p.Pro90Leu Uncertain significance ★ ⚠ same residue
- HAND2 p.Ala24_Ala32del Conflicting classifications of pathogenicity ★ same type
- HAND2 p.Ala25_Ala32del Uncertain significance ★ same type
- HAND2 p.Ala26_Ala32del Conflicting classifications of pathogenicity ★ same type
- HAND2 p.Ala27_Ala32del Uncertain significance ★ same type
- HAND2 p.Ala28_Ala32del Uncertain significance ★ same type
- HAND2 p.Tyr80fs 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/hand2-p-pro90fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown