HECW2 p.Val320=
c.960G>A · VCV4959275
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
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 -0.4 | GERP -1, phastCons 0.074 |
| Overall | ||
| CADD | 8.505 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- HECW2
- Protein
- p.Val320=
- Coding
- c.960G>A
- MANE Select
- NM_001348768
- Type
- single nucleotide variant
- Location
- chr2:196320364 (GRCh38)
- Gene constraint
- LOEUF 0.498 · pLI 0.86 (gnomAD)
- Structure
- AlphaFold pLDDT 62.07 · 2 PDB
Similar variants
- HECW2 p.Arg1191Gln Pathogenic ★★ same type
- HECW2 p.Arg1191Trp Likely pathogenic ★★ same type
- HECW2 p.Arg1330Trp Pathogenic ★★ same type
- HECW2 p.Arg1495Ser Pathogenic/Likely pathogenic ★★ same type
- HECW2 p.Asn1199Lys Pathogenic/Likely pathogenic ★★ same type
- HECW2 p.Asn1199Ser Likely pathogenic ★★ ⚠ same type
- HECW2 p.Leu1448Ser Likely pathogenic ★★ same type
- HECW2 p.Ser1504Tyr Likely pathogenic ★★ 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/hecw2-p-val320 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown