ARSI p.Pro439=
c.1317G>A · rs111413198 · VCV772129
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0134%, eas)
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 -15 | GERP -5.1 |
| Overall | ||
| CADD | 0.472 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0134%
East Asian · 6/44,868 alleles
Filtering AF
0.00579%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00394%
Overall
0.00161%
26/1,610,226 alleles · ultra-rare
exomes 25/1,457,874 · genomes 1/152,352 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0134% | 7,478 |
| Remaining individualsnot grpmax-eligible | 0.00641% | 15,595 |
| African / African-American | 0.00267% | 37,518 |
| South Asian | 0.00221% | 45,329 |
| European (non-Finnish) | 0.00102% | 98,216 |
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
- ARSI
- Protein
- p.Pro439=
- Coding
- c.1317G>A
- MANE Select
- NM_001012301
- dbSNP
- rs111413198
- Type
- single nucleotide variant
- Location
- chr5:150297607 (GRCh38)
- Gene constraint
- LOEUF 1.403 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 87.35
Similar variants
- ARSI p.Ala216Thr Uncertain significance ★★ ⚠ same type
- ARSI p.Ala259Val Uncertain significance ★★ ⚠ same type
- ARSI p.Ala264Thr Uncertain significance ★★ ⚠ same type
- ARSI p.Ala399Asp Uncertain significance ★★ ⚠ same type
- ARSI p.Ala414Ser Uncertain significance ★★ ⚠ same type
- ARSI p.Ala414Thr Uncertain significance ★★ ⚠ same type
- ARSI p.Ala78Thr Uncertain significance ★★ ⚠ same type
- ARSI p.Arg117Cys 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/arsi-p-pro439 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown