ADCK2 p.Thr401=
c.1203G>A · rs141910091 · VCV2658021
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.297%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| REVEL | 0.064 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | Δ0.26 | donor loss, 1 bp away · masked 0 · deltas |
| Constraint at this position | ||
| Conservation | phyloP -14 | GERP -7.5 |
| Overall | ||
| CADD | 0.007 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.297%
South Asian · 270/91,062 alleles
Filtering AF
0.267%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.256%
Overall
0.0227%
367/1,613,938 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.297% | 337 |
| African / African-American | 0.0267% | 3,750 |
| Remaining individualsnot grpmax-eligible | 0.0256% | 3,906 |
| Middle Eastern | 0.0165% | 6,060 |
| East Asian | 0.00891% | 11,219 |
| European (non-Finnish) | 0.00458% | 21,851 |
| Admixed American | 0.00333% | 29,997 |
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
- ADCK2
- Protein
- p.Thr401=
- Coding
- c.1203G>A
- MANE Select
- NM_052853
- dbSNP
- rs141910091
- Type
- single nucleotide variant
- Location
- chr7:140679277 (GRCh38)
- Gene constraint
- LOEUF 0.921 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 72.45
- Residue 401
- the protein kinase domain; a UniProt-annotated variant site (found in a patient with slow and progressive proximal muscle weakness with permanent myalgia both at rest and during muscular exertion which results in permanent disability; uncertain significance; decreased levels of coenzyme q10)
Similar variants
- ADCK2 p.Ala217Pro Uncertain significance ★ ⚠ same type
- ADCK2 p.Ala293Gly Uncertain significance ★ ⚠ same type
- ADCK2 p.Ala293Val Uncertain significance ★ ⚠ same type
- ADCK2 p.Ala319Thr Uncertain significance ★ ⚠ same type
- ADCK2 p.Ala465Val Uncertain significance ★ ⚠ same type
- ADCK2 p.Ala510Thr Uncertain significance ★ ⚠ same type
- ADCK2 p.Ala78Ser Uncertain significance ★ ⚠ same type
- ADCK2 p.Arg292Trp 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/adck2-p-thr401 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown