ATAD1 p.Arg338=
c.1012C>A · rs1470602790 · VCV1993768
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.22 | acceptor loss · deltas |
|---|---|---|
| Pangolin | Δ0.20 | loss · gain 0.01 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 12 | GERP 0.93, phastCons 1 |
| Overall | ||
| CADD | 6.908 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- ATAD1
- Protein
- p.Arg338=
- Coding
- c.1012C>A
- MANE Select
- NM_001321967
- dbSNP
- rs1470602790
- Type
- single nucleotide variant
- Location
- chr10:87754761 (GRCh38)
- Gene constraint
- LOEUF 0.505 · pLI 0.98 (gnomAD)
- Structure
- AlphaFold pLDDT 84.05 · 2 PDB
- Residue 338
- an α-helix; a UniProt-annotated variant site (in hkpx4; severely decreased atad1 mrna expression in lymphoblastoid cells derived from the patient compared to an unaffected control)
Similar variants
- ATAD1 p.Arg338Gln Uncertain significance ★★ ⚠ same residue
- ATAD1 p.Arg338Trp Uncertain significance ★★ ⚠ same residue
- ATAD1 p.Glu276Ter Pathogenic/Likely pathogenic ★★ same type
- ATAD1 p.Ala339Val Uncertain significance ★★ ⚠ same type
- ATAD1 p.Ala55Thr Uncertain significance ★★ ⚠ same type
- ATAD1 p.Asp164Asn Uncertain significance ★★ ⚠ same type
- ATAD1 p.Gln185Glu Uncertain significance ★★ ⚠ same type
- ATAD1 p.Gln352Pro 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/atad1-p-arg338 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown