CDC73 p.Ala2fs
c.4del · rs1060500020 · VCV403893
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function in a haploinsufficient gene (ClinGen) |
|---|---|---|
| NMD | predicted | premature termination codon in exon 1 of 17 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 7.3 | GERP 1.5, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.
Variant & gene context
- Gene
- CDC73
- Protein
- p.Ala2fs
- Coding
- c.4del
- MANE Select
- NM_024529
- dbSNP
- rs1060500020
- Type
- Deletion
- Location
- chr1:193122203 (GRCh38)
- Gene constraint
- LOEUF 0.42 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 73.94 · 21 PDB
- Residue 2
- a UniProt-annotated variant site (found in parathyroid adenoma samples; somatic mutation; parathyroid adenoma samples are from a patient with isolated hyperparathyroidism who also carries germline mutation p-91); a modified residue (n-acetylalanine)
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 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.His528_Leu529insTer Uncertain significance ★★ same condition
- CDC73 c.1031-12del Benign/Likely benign ★★ same condition
- CDC73 c.1067-4del Likely benign ★★ same condition
- CDC73 c.1560-11del 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-p-ala2fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown