HAL p.Pro652=
c.1956G>A · rs112610390 · VCV3043109
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0423%, eas)
Conditions
1
HAL-related disorder
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 -2.6 | GERP -2.9 |
| Overall | ||
| CADD | 9.221 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0423%
East Asian · 19/44,892 alleles
Filtering AF
0.0276%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.023%
Overall
0.0057%
92/1,613,864 alleles · ultra-rare
exomes 86/1,461,748 · genomes 6/152,116 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0423% | 2,363 |
| European (non-Finnish) | 0.00602% | 16,619 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,478 |
| African / African-American | 0.00134% | 74,898 |
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
- HAL
- Protein
- p.Pro652=
- Coding
- c.1956G>A
- MANE Select
- NM_002108
- dbSNP
- rs112610390
- Type
- single nucleotide variant
- Location
- chr12:95974250 (GRCh38)
- Gene constraint
- LOEUF 1.213 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 90.83
Disease context
HAL-related disorder
Similar variants
- HAL c.248-5T>C Likely benign same condition
- HAL p.Ala526= Likely benign same condition
- HAL p.Ile600= Likely benign same condition
- HAL p.Pro95= Likely benign same condition
- HAL c.*392C>T Uncertain significance ★★ same type
- HAL p.Arg9Cys Uncertain significance ★★ ⚠ same type
- HAL p.Asn476Lys Uncertain significance ★★ ⚠ same type
- HAL p.Glu472Lys 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/hal-p-pro652 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown