CASR p.Lys709=
c.2127G>A · rs2473278125 · VCV1977016
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
2
autosomal dominant hypocalcemia 1
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 4 | GERP 1.2, phastCons 1 |
| Overall | ||
| CADD | 7.766 | PHRED · no single calibrated threshold — expert panels disagree |
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
- CASR
- Protein
- p.Lys709=
- Coding
- c.2127G>A
- MANE Select
- NM_000388
- dbSNP
- rs2473278125
- Type
- single nucleotide variant
- Location
- chr3:122284081 (GRCh38)
- Gene constraint
- LOEUF 0.469 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 76.01 · 31 PDB
- Residue 709
- a UniProt-annotated variant site (in hhc1; impaired homodimerization; impaired cell membrane localization); the 'intracellular loop 2 (icl2)' region
Similar variants
- CASR c.1378-1G>C Likely pathogenic ★★ same condition
- CASR c.1608+1G>A Likely pathogenic ★★ same condition
- CASR c.1609-2A>G Likely pathogenic ★★ same condition
- CASR c.186-1G>T Pathogenic ★★ same condition
- CASR c.493-2A>C Likely pathogenic ★★ same condition
- CASR p.Ala581Val Likely pathogenic ★★ ⚠ same condition
- CASR p.Ala835Asp Pathogenic/Likely pathogenic ★★ same condition
- CASR p.Arg172Gly Pathogenic/Likely 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/casr-p-lys709 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown