ARSG p.Thr462=
c.1386C>T · rs200226454 · VCV1622040
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0164%, mid)
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 -7.9 | GERP -3.5 |
| Overall | ||
| CADD | 0.315 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0164%
Middle Eastern · 1/6,084 alleles
Filtering AF
0.000953%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000787%
Overall
0.00136%
22/1,613,960 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0164% | 6,084 |
| East Asian | 0.00223% | 44,878 |
| European (non-Finnish) | 0.00153% | 65,557 |
| African / African-American | 0.00134% | 74,880 |
| South Asian | 0.0011% | 91,076 |
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
- ARSG
- Protein
- p.Thr462=
- Coding
- c.1386C>T
- MANE Select
- NM_001267727
- dbSNP
- rs200226454
- Type
- single nucleotide variant
- Location
- chr17:68420271 (GRCh38)
- Gene constraint
- LOEUF 0.996 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 91.90
Similar variants
- ARSG p.Thr462Ile Uncertain significance ★ ⚠ same residue
- ARSG c.1091+1G>A Likely pathogenic ★★ same type
- ARSG c.982+2T>G Likely pathogenic ★★ same type
- ARSG p.Ala180Val Uncertain significance ★★ ⚠ same type
- ARSG p.Ala262Val Uncertain significance ★★ ⚠ same type
- ARSG p.Ala313Val Uncertain significance ★★ ⚠ same type
- ARSG p.Ala374Pro Uncertain significance ★★ ⚠ same type
- ARSG p.Ala437Val 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/arsg-p-thr462 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown