ATP13A4 p.Asp565=
c.1695C>T · rs370317634 · VCV742745
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.015%, amr)
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 -2.9 | GERP -3 |
| Overall | ||
| CADD | 0.531 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.015%
Admixed American · 9/60,004 alleles
Filtering AF
0.00773%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00578%
Overall
0.00304%
49/1,613,954 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.015% | 6,667 |
| East Asian | 0.00446% | 22,441 |
| European (non-Finnish) | 0.00288% | 34,706 |
| African / African-American | 0.00267% | 37,439 |
| South Asian | 0.0022% | 45,539 |
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
- ATP13A4
- Protein
- p.Asp565=
- Coding
- c.1695C>T
- MANE Select
- NM_032279
- dbSNP
- rs370317634
- Type
- single nucleotide variant
- Location
- chr3:193457445 (GRCh38)
- Gene constraint
- LOEUF 0.896 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 80.48
Similar variants
- ATP13A4 p.Glu646Asp Benign ★★ same type
- ATP13A4 p.Gly827= Benign ★★ same type
- ATP13A4 p.His61Arg Likely benign ★★ same type
- ATP13A4 p.Ile181Met Benign ★★ ⚠ same type
- ATP13A4 p.Leu1135= Benign ★★ same type
- ATP13A4 p.Leu983= Benign ★★ same type
- ATP13A4 p.Ser1191= Benign ★★ same type
- ATP13A4 p.Thr363= Benign ★★ 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/atp13a4-p-asp565 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown