HELLS p.Glu157del
c.469_471del · rs768376602 · VCV1499848
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00138%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 6.8 | GERP 1.1, phastCons 1 |
| Overall | ||
| CADD | 16.02 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00138%
African / African-American · 1/72,566 alleles
Filtering AF
0.000389%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000282%
Overall
0.000667%
10/1,499,422 alleles · very rare
exomes 8/1,347,224 · genomes 2/152,198 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00138% | 72,566 |
| European (non-Finnish) | 0.000827% | 120,873 |
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
- HELLS
- Protein
- p.Glu157del
- Coding
- c.469_471del
- MANE Select
- NM_018063
- dbSNP
- rs768376602
- Type
- Deletion
- Location
- chr10:94571419 (GRCh38)
- Gene constraint
- LOEUF 0.587 · pLI 0.63 (gnomAD)
- Structure
- AlphaFold pLDDT 68.76 · 4 PDB
Similar variants
- HELLS p.Arg129fs Pathogenic ★ same type
- HELLS p.Glu239fs Pathogenic ★ same type
- HELLS p.Ser164_Ser165insTer Likely pathogenic ★ same type
- HELLS p.Lys156del Uncertain significance ★ same type
- HELLS c.1033-5del Benign ★ same type
- HELLS c.1767+18_1767+23del Likely benign ★ same type
- HELLS c.1768-6_1768-4del Likely benign ★ same type
- HELLS c.1851+11del Benign ★ 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/hells-p-glu157del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown