CDC5L p.Ala498=
c.1494C>T · VCV3829873
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00534%, afr)
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 -9.1 | GERP -4.9 |
| Overall | ||
| CADD | 1.205 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00534%
African / African-American · 4/74,846 alleles
Filtering AF
0.00267%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00236%
Overall
0.00335%
54/1,613,620 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00534% | 18,711 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,822 |
| South Asian | 0.00439% | 22,765 |
| European (non-Finnish) | 0.00356% | 28,091 |
| East Asian | 0.00223% | 44,866 |
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.Ala498=
- Coding
- c.1494C>T
- MANE Select
- NM_001253
- Type
- single nucleotide variant
- Location
- chr6:44424508 (GRCh38)
- Gene constraint
- LOEUF 0.26 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 74.94 · 41 PDB
- Residue 498
- the 'interaction with ppp1r8' region
Similar variants
- CDC5L p.Ala93= Benign ★★ same type
- CDC5L p.Asp236= Benign ★★ same type
- CDC5L p.Leu721= Benign ★★ same type
- CDC5L p.Ala234Val Uncertain significance ★ ⚠ same type
- CDC5L p.Ala457Thr Uncertain significance ★ ⚠ same type
- CDC5L p.Ala485Thr Uncertain significance ★ ⚠ same type
- CDC5L p.Arg202Lys Uncertain significance ★ ⚠ same type
- CDC5L p.Arg202Thr 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/cdc5l-p-ala498 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown