rs1553769059

Variant names:

• chr3-122284198-G-CC
• rs1553769059
• NM_000388.4:c.2244delGinsCC

Your query was ambiguous. Multiple possible variants found:

• chr3-122284197-CG-CCC
• chr3-122284197-CG-CGG

Variant summary

Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1 PM2 PP5_Moderate

The NM_000388.4(CASR):​c.2244delGinsCC​(p.Ser749LeufsTer11) variant causes a frameshift, synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Likely pathogenic (★). Synonymous variant affecting the same amino acid position (i.e. P748P) has been classified as Benign.

• Frequency: Genomes: not found (cov: 32)
• Consequence: CASR NM_000388.4 frameshift, synonymous
• Clinical Significance: Likely pathogenic criteria provided, single submitter P:1
• Conservation: PhyloP100: -2.53

Genes affected

CASR (HGNC:1514): (calcium sensing receptor) The protein encoded by this gene is a plasma membrane G protein-coupled receptor that senses small changes in circulating calcium concentration. The encoded protein couples this information to intracellular signaling pathways that modify parathyroid hormone secretion or renal cation handling, and thus this protein plays an essential role in maintaining mineral ion homeostasis. Mutations in this gene are a cause of familial hypocalciuric hypercalcemia, neonatal severe hyperparathyroidism, and autosomal dominant hypocalcemia. [provided by RefSeq, Aug 2017]

ACMG classification

Verdict is Pathogenic. Variant got 12 ACMG points.

• PVS1: Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant is located in the 3'-most exon, not predicted to undergo nonsense mediated mRNA decay. There are 61 pathogenic variants in the truncated region.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 3-122284198-G-CC is Pathogenic according to our data. Variant chr3-122284198-G-CC is described in ClinVar as [Likely_pathogenic]. Clinvar id is 2636276.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CASR	NM_000388.4	c.2244delGinsCC	p.Ser749LeufsTer11	frameshift_variant, synonymous_variant	Exon 7 of 7	ENST00000639785.2	NP_000379.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CASR	ENST00000639785.2	c.2244delGinsCC	p.Ser749LeufsTer11	frameshift_variant, synonymous_variant	Exon 7 of 7	1	NM_000388.4	ENSP00000491584.2
CASR	ENST00000498619.4	c.2274delGinsCC	p.Ser759LeufsTer11	frameshift_variant, synonymous_variant	Exon 7 of 7	1		ENSP00000420194.1
CASR	ENST00000638421.1	c.2244delGinsCC	p.Ser749LeufsTer11	frameshift_variant, synonymous_variant	Exon 7 of 7	5		ENSP00000492190.1
CASR	ENST00000490131.7	c.2013delGinsCC	p.Ser672LeufsTer11	frameshift_variant, synonymous_variant	Exon 5 of 5	5		ENSP00000418685.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 69

GnomAD4 genome Cov.: 32

ClinVar

Significance: Likely pathogenic

Submissions summary: Pathogenic:1

Revision: criteria provided, single submitter

Submissions by phenotype

CASR-related disorder Pathogenic:1

Sep 01, 2022

PreventionGenetics, part of Exact Sciences

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The CASR c.2274delinsCC variant is predicted to result in a frameshift and premature protein termination (p.Ser759Leufs*11). To our knowledge, this variant has not been reported in the literature or in a large population database (http://gnomad.broadinstitute.org), indicating this variant is rare. Frameshift variants in CASR are expected to be pathogenic. This variant is interpreted as likely pathogenic. -

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1553769059; hg19: chr3-122003045;