Is CASR p.Arg227= (c.681A>G) pathogenic?

CASR p.Arg227= (c.681A>G) is classified Likely benign in CASR (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-01-23). Very rare (popmax 0.000424%, nfe); Associated with autosomal dominant hypocalcemia 1.

What condition is associated with CASR p.Arg227= (c.681A>G)?

CASR p.Arg227= (c.681A>G) is associated with autosomal dominant hypocalcemia 1, familial hypocalciuric hypercalcemia (ClinVar).

How common is CASR p.Arg227= (c.681A>G) in the general population?

CASR p.Arg227= (c.681A>G) is very rare (popmax 0.000424%, nfe) (gnomAD).

CASR p.Arg227=

c.681A>G · rs766844902 · VCV1137985

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 0.000424%, nfe)

Conditions

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 -0.049	GERP -2.4, phastCons 0.013
Overall
CADD	6.988	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.000424% European (non-Finnish) · 5/1,180,044 alleles

Filtering AF 0.000124% ClinGen BA1/BS1 input FAF95, joint · FAF99 9e-05%

Overall 0.000342% 5/1,461,882 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: CASR
Protein: p.Arg227=
Coding: c.681A>G
MANE Select: NM_000388
dbSNP: rs766844902
Type: single nucleotide variant
Location: chr3:122261716 (GRCh38)
Gene constraint: LOEUF 0.469 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 76.01 · 31 PDB
Residue 227: a UniProt-annotated variant site (in nshpt; decreased g protein-coupled receptor signaling pathway; does not affect cell membrane localization); a UniProt-annotated variant site (in hhc1; decreased g protein-coupled receptor signaling pathway; does not affect cell membrane localization); the 'ligand-binding 2 (lb2)' region; an α-helix

Full CASR gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

autosomal dominant hypocalcemia 1 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: familial hypocalciuric hypercalcemia

Similar variants

CASR p.Arg227Gln Pathogenic/Likely pathogenic ★★ ⚠ same residue
CASR p.Arg227Leu Pathogenic ★★ ⚠ same residue
CASR p.Arg227Ter Pathogenic/Likely pathogenic ★★ same residue
CASR p.Arg227Gly Likely pathogenic ★ ⚠ same residue
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

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-arg227 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown