CDC5L p.His618=
c.1854T>C · rs11572023 · VCV787834
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 2.82%, 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 0.88 | GERP 1.1, phastCons 1 |
| Overall | ||
| CADD | 7.389 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.82%
African / African-American · 2,113/75,008 alleles
Filtering AF
2.72%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.68%
Overall
0.145%
2,341/1,612,882 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.82% | 35 |
| Admixed American | 0.173% | 576 |
| Remaining individualsnot grpmax-eligible | 0.15% | 665 |
| Middle Eastern | 0.0496% | 2,017 |
| South Asian | 0.0154% | 6,501 |
| European (non-Finnish) | 0.0011% | 90,712 |
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.His618=
- Coding
- c.1854T>C
- MANE Select
- NM_001253
- dbSNP
- rs11572023
- Type
- single nucleotide variant
- Location
- chr6:44426685 (GRCh38)
- Gene constraint
- LOEUF 0.26 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 74.94 · 41 PDB
- Residue 618
- the 'interaction with dapk3' region; an α-helix
Similar variants
- CDC5L p.His618Pro Uncertain significance ★ ⚠ same residue
- 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
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-his618 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown