CDC73 c.237+1G>C
Pathogenic
Single submitter
Classification
Pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
canonical splice-site (±1/±2)
predicted LoF
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
parathyroid gland carcinoma
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Consequence | canonical splice-site (±1/±2) | predicted loss-of-function in a haploinsufficient gene (ClinGen) |
|---|---|---|
| Splicing | ||
| Splice region | donor +1 | canonical splice dinucleotide (donor +1) · inside the BP7-excluded zone |
| SpliceAI | Δ1.00 | donor loss · deltas |
| Pangolin | Δ0.87 | loss · gain 0.04 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 12 | GERP 1.6, phastCons 1 |
| Overall | ||
| CADD | 34.0 | PHRED · no single calibrated threshold — expert panels disagree |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- CDC73
- Coding
- c.237+1G>C
- MANE Select
- NM_024529
- dbSNP
- rs794727303
- Type
- single nucleotide variant
- Location
- chr1:193125218 (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-237-plus-1g-c (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown