ATN1 p.Pro903=
c.2709A>G · rs2542637358 · VCV2642655
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00668%, 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 -4.7 | GERP -3.9 |
| Overall | ||
| CADD | 1.195 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00668%
East Asian · 3/44,884 alleles
Filtering AF
0.00177%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000891%
Overall
0.000205%
3/1,461,850 alleles · very rare
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
- ATN1
- Protein
- p.Pro903=
- Coding
- c.2709A>G
- MANE Select
- NM_001940
- dbSNP
- rs2542637358
- Type
- single nucleotide variant
- Location
- chr12:6938672 (GRCh38)
- Gene constraint
- LOEUF 0.352 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 49.25
Similar variants
- ATN1 p.Pro903Thr Uncertain significance ★ same residue
- ATN1 p.His1052Pro Pathogenic/Likely pathogenic ★★ same type
- ATN1 p.Ser1059Leu Pathogenic/Likely pathogenic ★★ same type
- ATN1 p.Arg1152Cys Uncertain significance ★★ ⚠ same type
- ATN1 p.Asn422Ser Uncertain significance ★★ ⚠ same type
- ATN1 p.Glu814Gly Uncertain significance ★★ ⚠ same type
- ATN1 p.Met335Ile Uncertain significance ★★ ⚠ same type
- ATN1 p.Pro185Ala 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/atn1-p-pro903 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown