ATRN p.Ala1413=
c.4239C>T · VCV3651341
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0587%, 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 -7.2 | GERP -4.1 |
| Overall | ||
| CADD | 0.147 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0587%
South Asian · 53/90,342 alleles
Filtering AF
0.046%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0415%
Overall
0.00664%
107/1,611,718 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0587% | 1,705 |
| Middle Eastern | 0.0165% | 6,076 |
| East Asian | 0.00669% | 14,947 |
| Remaining individualsnot grpmax-eligible | 0.00481% | 20,797 |
| African / African-American | 0.00401% | 24,967 |
| European (non-Finnish) | 0.00373% | 26,798 |
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.Ala1413=
- Coding
- c.4239C>T
- MANE Select
- NM_139321
- Type
- single nucleotide variant
- Location
- chr20:3646796 (GRCh38)
- Gene constraint
- LOEUF 0.395 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 79.27
Similar variants
- 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
- ATRN p.Asn300Thr Uncertain significance ★★ ⚠ same type
- ATRN p.Asp508Asn 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-ala1413 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown