ATAD5 p.Leu1237=
c.3709T>C · rs555255925 · VCV722470
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.281%, mid)
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 0.012 | GERP -2.9, phastCons 0.008 |
| Overall | ||
| CADD | 6.369 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.281%
Middle Eastern · 17/6,044 alleles
Filtering AF
0.179%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.147%
Overall
0.017%
274/1,608,104 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.281% | 356 |
| South Asian | 0.119% | 838 |
| Remaining individualsnot grpmax-eligible | 0.0305% | 3,276 |
| Admixed American | 0.0184% | 5,433 |
| European (non-Finnish) | 0.00995% | 10,050 |
| African / African-American | 0.00267% | 37,428 |
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
- ATAD5
- Protein
- p.Leu1237=
- Coding
- c.3709T>C
- MANE Select
- NM_024857
- dbSNP
- rs555255925
- Type
- single nucleotide variant
- Location
- chr17:30876475 (GRCh38)
- Gene constraint
- LOEUF 0.417 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 46.76 · 4 PDB
Similar variants
- ATAD5 c.4013-8G>A Benign ★★ same type
- ATAD5 p.Asp826= Likely benign ★★ same type
- ATAD5 p.Ala1326Thr Uncertain significance ★ ⚠ same type
- ATAD5 p.Ala1459Thr Uncertain significance ★ ⚠ same type
- ATAD5 p.Ala1539Pro Uncertain significance ★ ⚠ same type
- ATAD5 p.Ala1711Val Uncertain significance ★ ⚠ same type
- ATAD5 p.Ala326Val Uncertain significance ★ ⚠ same type
- ATAD5 p.Ala414Thr 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/atad5-p-leu1237 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown