ATAD3B p.Cys641=
c.1923C>T · rs146505120 · VCV725969
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0957%, 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 -2.3 | GERP -1.1 |
| Overall | ||
| CADD | 0.52 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0957%
South Asian · 84/87,744 alleles
Filtering AF
0.0792%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0731%
Overall
0.0266%
423/1,588,416 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0957% | 1,045 |
| European (non-Finnish) | 0.027% | 3,702 |
| Middle Eastern | 0.0219% | 4,572 |
| Remaining individualsnot grpmax-eligible | 0.0163% | 6,131 |
| Finnishnot grpmax-eligible | 0.00966% | 10,357 |
| Admixed American | 0.00516% | 19,388 |
| African / African-American | 0.00403% | 24,835 |
| East Asian | 0.00224% | 44,732 |
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
- ATAD3B
- Protein
- p.Cys641=
- Coding
- c.1923C>T
- MANE Select
- NM_031921
- dbSNP
- rs146505120
- Type
- single nucleotide variant
- Location
- chr1:1495793 (GRCh38)
- Gene constraint
- LOEUF 1.152 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 77.69
Similar variants
- ATAD3B c.445-11C>G Benign ★★ same type
- ATAD3B p.Ala71Ser Benign ★★ same type
- ATAD3B p.Phe274Tyr Benign/Likely benign ★★ same type
- ATAD3B p.Pro639Ser Benign ★★ same type
- ATAD3B p.Val259= Likely benign ★★ same type
- ATAD3B c.1090-3C>T Uncertain significance ★ same type
- ATAD3B c.325C>T Uncertain significance ★ ⚠ same type
- ATAD3B c.623G>A 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/atad3b-p-cys641 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown