CDC5L p.Ala516=
c.1548T>C · rs762774387 · VCV3031164
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0022%, nfe)
Conditions
1
CDC5L-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 -3.1 | GERP -4.9 |
| Overall | ||
| CADD | 5.321 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0022%
European (non-Finnish) · 26/1,179,890 alleles
Filtering AF
0.00153%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0013%
Overall
0.00161%
26/1,613,778 alleles · very rare
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
- CDC5L
- Protein
- p.Ala516=
- Coding
- c.1548T>C
- MANE Select
- NM_001253
- dbSNP
- rs762774387
- Type
- single nucleotide variant
- Location
- chr6:44424562 (GRCh38)
- Gene constraint
- LOEUF 0.26 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 74.94 · 41 PDB
- Residue 516
- the 'interaction with dapk3' region; the 'interaction with ppp1r8' region; an α-helix
Disease context
CDC5L-related disorder
Similar variants
- CDC5L p.Arg426Gln Uncertain significance ★ ⚠ same condition
- CDC5L p.Met582Arg Uncertain significance ★ ⚠ same condition
- CDC5L p.Arg49= Uncertain significance same condition
- CDC5L c.904-10G>A Likely benign same condition
- CDC5L c.-2A>G Likely benign same condition
- CDC5L c.-7C>T Likely benign same condition
- CDC5L p.Ala22= Likely benign same condition
- CDC5L p.Ala305= 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/cdc5l-p-ala516 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown