ATRN p.Ile1093=
c.3279A>C · rs756404864 · VCV2970938
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 2.8 | GERP -3.7, phastCons 1 |
| Overall | ||
| CADD | 7.91 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0134%
East Asian · 6/44,898 alleles
Filtering AF
0.00579%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00394%
Overall
0.000434%
7/1,614,076 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0134% | 7,483 |
| South Asian | 0.0011% | 91,086 |
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
- ATRN
- Protein
- p.Ile1093=
- Coding
- c.3279A>C
- MANE Select
- NM_139321
- dbSNP
- rs756404864
- Type
- single nucleotide variant
- Location
- chr20:3591263 (GRCh38)
- Gene constraint
- LOEUF 0.395 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 79.27
- Residue 1093
- the laminin egf-like 1 domain; a disulfide bond
Similar variants
- ATRN p.Ile1093Leu Uncertain significance ★★ ⚠ same residue
- ATRN p.Ile1093Val Benign ★ same residue
- ATRN p.Ala438Gly Uncertain significance ★★ ⚠ same type
- ATRN p.Ala87Val Uncertain significance ★★ ⚠ same type
- ATRN p.Arg1417Gln Uncertain significance ★★ ⚠ same type
- ATRN p.Arg173His Uncertain significance ★★ ⚠ same type
- ATRN p.Asn1035Ser Uncertain significance ★★ ⚠ same type
- ATRN p.Asn213Ser 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/atrn-p-ile1093 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown