EXT1 p.Arg86=
c.256C>A · rs760899584 · VCV509106
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.48e-05%, nfe)
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 9.9 | GERP 4.1, phastCons 1 |
| Overall | ||
| CADD | 14.47 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.48e-05%
European (non-Finnish) · 1/1,179,590 alleles
Overall
6.2e-05%
1/1,613,590 alleles · very rare
exomes 1/1,461,320 · genomes 0/152,270 · joint denominator
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
- EXT1
- Protein
- p.Arg86=
- Coding
- c.256C>A
- MANE Select
- NM_000127
- dbSNP
- rs760899584
- Type
- single nucleotide variant
- Location
- chr8:118110791 (GRCh38)
- Gene constraint
- LOEUF 0.339 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 84.67 · 6 PDB
Similar variants
- EXT1 p.Arg86Ter Pathogenic/Likely pathogenic ★★ same residue
- EXT1 c.1056+1G>A Pathogenic ★★ same type
- EXT1 c.1056+1G>T Pathogenic ★★ same type
- EXT1 c.1165-1G>A Pathogenic ★★ same type
- EXT1 c.1285-1G>C Pathogenic ★★ same type
- EXT1 c.1417+1G>A Pathogenic ★★ same type
- EXT1 c.1417+1G>T Pathogenic ★★ same type
- EXT1 c.1418-1G>A 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/ext1-p-arg86 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown