CDC45 p.Ser264=
c.792C>T · rs61756282 · VCV746795
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0276%, nfe)
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 -9.2 | GERP -3.1 |
| Overall | ||
| CADD | 2.1 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0276%
European (non-Finnish) · 326/1,179,964 alleles
Filtering AF
0.0251%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0241%
Overall
0.0219%
354/1,614,146 alleles · ultra-rare
exomes 336/1,461,776 · genomes 18/152,370 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0276% | 3,620 |
| Remaining individualsnot grpmax-eligible | 0.0224% | 4,465 |
| Admixed American | 0.0133% | 7,504 |
| African / African-American | 0.004% | 25,023 |
| East Asian | 0.00223% | 44,884 |
| Finnishnot grpmax-eligible | 0.00156% | 64,020 |
| South Asian | 0.0011% | 91,090 |
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
- CDC45
- Protein
- p.Ser264=
- Coding
- c.792C>T
- MANE Select
- NM_003504
- dbSNP
- rs61756282
- Type
- single nucleotide variant
- Location
- chr22:19505449 (GRCh38)
- Gene constraint
- LOEUF 0.77 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 92.59 · 7 PDB
- Residue 264
- a UniProt-annotated variant site (in mgors7; uncertain significance)
Similar variants
- CDC45 p.Ser264Tyr Uncertain significance ★ same residue
- CDC45 p.Ser264fs Pathogenic ★ same residue
- CDC45 p.Pro463Leu Pathogenic/Likely pathogenic ★★ ⚠ same type
- CDC45 c.653+4C>T Uncertain significance ★★ same type
- CDC45 p.Ala373Val Uncertain significance ★★ ⚠ same type
- CDC45 p.Ala38Asp Uncertain significance ★★ ⚠ same type
- CDC45 p.Arg157His Uncertain significance ★★ ⚠ same type
- CDC45 p.Arg175Gln 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/cdc45-p-ser264 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown