ATAD5 p.Ser1678=
c.5034T>C · rs193221883 · VCV3053616
Benign
No assertion criteria
Classification
Benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.595%, amr)
Conditions
1
ATAD5-related disorder
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 -1.8 | GERP -3.7 |
| Overall | ||
| CADD | 1.289 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.595%
Admixed American · 357/60,014 alleles
Filtering AF
0.544%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.524%
Overall
0.0228%
368/1,614,036 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.595% | 168 |
| Remaining individualsnot grpmax-eligible | 0.0112% | 8,928 |
| African / African-American | 0.00133% | 75,058 |
| European (non-Finnish) | 0.000254% | 393,309 |
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.Ser1678=
- Coding
- c.5034T>C
- MANE Select
- NM_024857
- dbSNP
- rs193221883
- Type
- single nucleotide variant
- Location
- chr17:30893887 (GRCh38)
- Gene constraint
- LOEUF 0.417 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 46.76 · 4 PDB
- Residue 1678
- the 'interaction with rad51 and rfc5' region
Disease context
ATAD5-related disorder
Similar variants
- ATAD5 c.2956+9T>C Likely benign same condition
- ATAD5 c.5456+7G>C Benign same condition
- ATAD5 c.5457-7T>G Likely benign same condition
- ATAD5 p.Arg1448Cys Benign same condition
- ATAD5 p.Arg249Lys Benign same condition
- ATAD5 p.Arg52= Likely benign same condition
- ATAD5 p.Asn1767Ser Benign same condition
- ATAD5 p.Asn699His Benign same condition
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-ser1678 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown