CDC73 c.1066+19T>C
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.72e-05%, nfe)
Conditions
1
parathyroid gland carcinoma
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +19 | near-intronic (+19 nt from the splice site) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -1 | GERP -2.5 |
| Non-coding constraint | Z -0.23 | 1 kb window · o/e 1.02 · regional · uncalibrated |
| Overall | ||
| CADD | 8.422 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.72e-05%
European (non-Finnish) · 1/1,147,280 alleles
Overall
7.08e-05%
1/1,412,384 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
- CDC73
- Coding
- c.1066+19T>C
- MANE Select
- NM_024529
- dbSNP
- rs2527455820
- Type
- single nucleotide variant
- Location
- chr1:193212119 (GRCh38)
- Gene constraint
- LOEUF 0.42 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 73.94 · 21 PDB
Disease context
parathyroid gland carcinoma — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Parathyroid carcinoma (Orphanet):
- Inheritance
- Not applicable
- Onset
- Adult
- Prevalence
- <1 / 1 000 000 (Europe)
Similar variants
- CDC73 c.1030+2T>C Likely pathogenic ★★ same condition
- CDC73 c.131+1G>A Pathogenic/Likely pathogenic ★★ same condition
- CDC73 c.237+1G>A Pathogenic ★★ same condition
- CDC73 c.423+1G>A Pathogenic ★★ same condition
- CDC73 c.513-1G>A Likely pathogenic ★★ same condition
- CDC73 p.Arg120Ter Pathogenic ★★ same condition
- CDC73 p.Arg126Ter Pathogenic/Likely pathogenic ★★ same condition
- CDC73 p.Arg139Ter Pathogenic ★★ 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/cdc73-c-1066-plus-19t-c (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown