CDC73 c.512+1del
Likely pathogenic
Single submitter
Classification
Likely pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
canonical splice-site (±1/±2)
predicted LoF
gnomAD v4.1
Rare
Conditions
3
hyperparathyroidism 2 with jaw tumors
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation 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 | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 5.3 | GERP 0.46, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- CDC73
- Coding
- c.512+1del
- MANE Select
- NM_024529
- Type
- Deletion
- Location
- chr1:193138173 (GRCh38)
- Gene constraint
- LOEUF 0.42 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 73.94 · 21 PDB
Disease context
hyperparathyroidism 2 with jaw tumors — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsAlso linked: hyperparathyroidism 1parathyroid gland carcinoma
For Hyperparathyroidism-jaw tumor syndrome (Orphanet):
- Inheritance
- Autosomal dominant
- Onset
- Adolescent, Adult
Similar variants
- CDC73 p.Arg171fs Pathogenic ★★ same condition
- CDC73 p.Asn82fs Pathogenic ★★ same condition
- CDC73 p.Glu81fs Pathogenic ★★ same condition
- CDC73 p.Lys209fs Pathogenic ★★ same condition
- CDC73 p.Ser174fs Pathogenic ★★ same condition
- CDC73 p.His528_Leu529insTer Uncertain significance ★★ same condition
- CDC73 c.1031-12del Benign/Likely benign ★★ same condition
- CDC73 c.1067-4del Likely benign ★★ 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-512-plus-1del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown