ATN1 p.Pro367=
c.1101A>G · rs138480639 · VCV2570817
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.54%, sas)
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 -2.1 | GERP -3.2 |
| Overall | ||
| CADD | 1.491 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.54%
South Asian · 1,402/91,060 alleles
Filtering AF
1.47%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.45%
Overall
0.41%
6,613/1,613,556 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 1.54% | 65 |
| Middle Eastern | 1.52% | 66 |
| European (non-Finnish) | 0.396% | 252 |
| Remaining individualsnot grpmax-eligible | 0.384% | 260 |
| Admixed American | 0.15% | 667 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0845% | 1,184 |
| African / African-American | 0.0775% | 1,290 |
| Finnishnot grpmax-eligible | 0.0454% | 2,205 |
| East Asian | 0.00446% | 22,423 |
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.Pro367=
- Coding
- c.1101A>G
- MANE Select
- NM_001940
- dbSNP
- rs138480639
- Type
- single nucleotide variant
- Location
- chr12:6936368 (GRCh38)
- Gene constraint
- LOEUF 0.352 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 49.25
- Residue 367
- the 'disordered' region
Similar variants
- 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
- ATN1 p.Pro720Ser 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-pro367 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown