3-122261697-C-T

Variant names:

• chr3-122261697-C-T
• rs397514728
• NM_000388.4:c.662C>T

Variant summary

Our verdict is Pathogenic. The variant received 15 ACMG points: 15P and 0B. PM1 PM2 PM5 PP2 PP5_Very_Strong

The NM_000388.4(CASR):​c.662C>T​(p.Pro221Leu) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P221S) has been classified as Pathogenic.

• Frequency: Genomes: not found (cov: 32)
• Consequence: CASR NM_000388.4 missense
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:12
• Conservation: PhyloP100: 6.14
• Publications: 27 publications found

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]

CASR Gene-Disease associations (from GenCC):

• autosomal dominant hypocalcemia 1

  Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Illumina, ClinGen, Labcorp Genetics (formerly Invitae)
• familial hypocalciuric hypercalcemia 1

  Inheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), ClinGen, Illumina, Orphanet, Genomics England PanelApp
• neonatal severe primary hyperparathyroidism

  Inheritance: AR, AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, ClinGen, Labcorp Genetics (formerly Invitae)
• autosomal dominant hypocalcemia

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• epilepsy, idiopathic generalized, susceptibility to, 8

  Inheritance: AD Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)
• epilepsy

  Inheritance: AD Classification: NO_KNOWN Submitted by: ClinGen

ACMG classification

Our verdict: Pathogenic. The variant received 15 ACMG points.

• PM1: In a hotspot region, there are 14 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 0 benign, 16 uncertain in NM_000388.4
• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr3-122261696-C-T is described in ClinVar as Pathogenic. ClinVar VariationId is 3068868.Status of the report is criteria_provided_single_submitter, 1 stars.
• PP2: Missense variant in the CASR gene, where missense mutations are typically associated with disease (based on misZ statistic). The gene has 114 curated pathogenic missense variants (we use a threshold of 10). The gene has 10 curated benign missense variants. Gene score misZ: 3.1237 (above the threshold of 3.09). Trascript score misZ: 4.8257 (above the threshold of 3.09). GenCC associations: The gene is linked to neonatal severe primary hyperparathyroidism, autosomal dominant hypocalcemia 1, familial hypocalciuric hypercalcemia 1, epilepsy, autosomal dominant hypocalcemia, epilepsy, idiopathic generalized, susceptibility to, 8.
• PP5: Variant 3-122261697-C-T is Pathogenic according to our data. Variant chr3-122261697-C-T is described in ClinVar as Pathogenic. ClinVar VariationId is 60667.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000388.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CASR	NM_000388.4	MANE Select	c.662C>T	p.Pro221Leu	missense	Exon 4 of 7	NP_000379.3
	CASR	NM_001178065.2		c.662C>T	p.Pro221Leu	missense	Exon 4 of 7	NP_001171536.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CASR	ENST00000639785.2	TSL:1 MANE Select	c.662C>T	p.Pro221Leu	missense	Exon 4 of 7	ENSP00000491584.2
	CASR	ENST00000498619.4	TSL:1	c.662C>T	p.Pro221Leu	missense	Exon 4 of 7	ENSP00000420194.1
	CASR	ENST00000638421.1	TSL:5	c.662C>T	p.Pro221Leu	missense	Exon 4 of 7	ENSP00000492190.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:12

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Pathogenic:4

Apr 01, 2021

CeGaT Center for Human Genetics Tuebingen

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Oct 31, 2024

GeneDx

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Published functional studies demonstrate a damaging effect: enhanced sensitivity and aberrant intracellular signaling (PMID: 25420019, 11701698, 20668040); Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis indicates that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 33057194, 35982159, 22789683, 12067826, 21645025, 22422767, 24297799, 25137426, 25420019, 11136551, 25039540, 26386835, 11701698, 20668040, 20119591, 24133354, 12733714)

Jan 14, 2015

Athena Diagnostics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Oct 20, 2023

Mayo Clinic Laboratories, Mayo Clinic

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

PP1_strong, PP2, PM2, PS3, PS4

Autosomal dominant hypocalcemia 1 Pathogenic:2

Jun 15, 2012

OMIM

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

Feb 25, 2025

3billion

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The variant is not observed in the gnomAD v4.1.0 dataset. Predicted Consequence/Location: Missense variant Functional studies provide strong evidence of the variant having a damaging effect on the gene or gene product (PMID: 22422767). In silico tool predictions suggest damaging effect of the variant on gene or gene product [REVEL: 0.68 (>=0.6, sensitivity 0.68 and specificity 0.92); 3Cnet: 0.99 (>0.75, sensitivity 0.96 and precision 0.92)]. The same nucleotide change resulting in the same amino acid change has been previously reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000060667 /PMID: 11136551). The variant has been reported to co-segregate with the disease in at least 7 similarly affected relatives/individuals in at least two unrelated families (PMID: 11136551). Different missense changes at the same codon (p.Pro221Gln, p.Pro221Ser) have been reported to be associated with CASR-related disorder (ClinVar ID: VCV000060668, VCV003068868 /PMID: 17698911, 9039332). Therefore, this variant is classified as Pathogenic according to the recommendation of ACMG/AMP guideline.

Autosomal dominant hypocalcemia Pathogenic:2

Sep 05, 2022

Molecular Genetics, Royal Melbourne Hospital

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change in CASR is predicted to replace proline with leucine at codon 221, p.(Pro221Leu). The proline residue is highly conserved (100 vertebrates, UCSC), and is located in the extracellular ANF receptor domain. There is a moderate physicochemical difference between proline and leucine. This variant is absent from the population database gnomAD v2.1 and v3.1. This is a recurrent variant that has been reported in multiple families with a clinical diagnosis of hypocalcemia and hypoparathyroidism and strong evidence for segregation with disease (PMID: 11136551, 12733714, 20668040, 22789683, 24133354). In vitro functional assays in mammalian cell lines showed enhanced receptor responsiveness to calcium concentrations indicating that this variant impacts protein function through a gain-of-function mechanism (PMID: 11136551, 25420019). Multiple lines of computational evidence have conflicting predictions for the missense substitution (3/6 algorithms predict deleterious). Based on the classification scheme RMH Modified ACMG Guidelines v1.5.1, this variant is classified as PATHOGENIC. Following criteria are met: PS4, PP1_Strong, PS3_Supporting, PM2_Supporting.

Nov 12, 2021

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant summary: CASR c.662C>T (p.Pro221Leu) results in a non-conservative amino acid change in the encoded protein sequence. Three of five in-silico tools predict a damaging effect of the variant on protein function. The variant was absent in 250832 control chromosomes (gnomAD). c.662C>T has been reported in the literature in multiple individuals affected with Autosomal Dominant Hypocalcemia and it was documented to segregate with disease in affected families (e.g. Conley_2000, Lienhardt_2001, Chikatsu_2003, Raue_2011, Kinoshita_2014). These data indicate that the variant is very likely to be associated with disease. Experimental evidence evaluating an impact on protein function demonstrated that the variant has an increased sensitivity to calcium compared to the wild-type, indicating that it is is an activating mutation of CASR (e.g. Conley_2000, Lienhardt_2001, Chikatsu_2003, Kinoshita_2014). Three ClinVar submitters (evaluation after 2014) cite the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.

Nephrolithiasis/nephrocalcinosis Pathogenic:1

Sep 12, 2023

Ambry Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.662C>T (p.P221L) alteration is located in exon 4 (coding exon 3) of the CASR gene. This alteration results from a C to T substitution at nucleotide position 662, causing the proline (P) at amino acid position 221 to be replaced by a leucine (L). Based on the available evidence, the CASR c.662C>T (p.P221L) alteration is classified as pathogenic for autosomal dominant CASR-related hypocalcemia; however, it is unlikely to be causative of autosomal recessive neonatal hyperparathyroidism and autosomal dominant hypocalciuric hypercalcemia. This variant was not reported in population-based cohorts in the Genome Aggregation Database (gnomAD). This variant has been detected in the heterozygous state in multiple individuals with CASR-related hypocalcemia and cosegregates with disease in several families (Conley, 2000; Lienhardt, 2001; Poppe, 2002; Chikatsu, 2003; Letz, 2010; Kim, 2010; Raue, 2011; Guarnieri, 2012; Hannan, 2012; Mitsui, 2014). This amino acid position is highly conserved in available vertebrate species. In vitro functional studies showed that this variant increases the sensitivity to extracellular calcium (Conley, 2000; Lienhardt, 2001; Chikatsu, 2003; Letz, 2010; Hannan, 2012). The in silico prediction for this alteration is inconclusive. Based on the available evidence, this alteration is classified as pathogenic.

CASR-related disorder Pathogenic:1

Jan 31, 2024

PreventionGenetics, part of Exact Sciences

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

The CASR c.662C>T variant is predicted to result in the amino acid substitution p.Pro221Leu. This variant has been repeatedly reported to be pathogenic for autosomal dominant hypocalcemia due to receptor activation (see for example Hannan et al. 2012. PubMed ID: 22422767; Guarnieri et al. 2012. PubMed ID: 22789683; Conley et al. 2000. PubMed ID: 11136551). Other amino acid substitutions at this position (p.Pro221Ser, p.Pro221Gln) have also been reported in patients with CASR-related disorders (Pearce et al. 1996. PubMed ID: 9039332; Nissen et al. 2007. PubMed ID: 17698911). This variant has not been reported in a large population database, indicating this variant is rare. This variant is interpreted as pathogenic.

Autosomal dominant hypocalcemia 1;C1809471:Familial hypocalciuric hypercalcemia Pathogenic:1

Jun 23, 2023

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change replaces proline, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 221 of the CASR protein (p.Pro221Leu). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with autosomal dominant hypocalcemia (PMID: 11136551, 12733714, 20119591, 21645025, 25137426). It has also been observed to segregate with disease in related individuals. This variant is also known as 1034C>T. ClinVar contains an entry for this variant (Variation ID: 60667). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. Experimental studies have shown that this missense change affects CASR function (PMID: 11136551, 12733714, 22422767, 24297799, 25420019). For these reasons, this variant has been classified as Pathogenic.

Autosomal dominant hypocalcemia 1;C0342637:Familial hypocalciuric hypercalcemia 1;C1832615:Neonatal severe primary hyperparathyroidism;C2752062:Epilepsy, idiopathic generalized, susceptibility to, 8 Pathogenic:1

Oct 23, 2021

Fulgent Genetics, Fulgent Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.71
BayesDel_addAF	Pathogenic	0.34	D
BayesDel_noAF	Pathogenic	0.24
CADD	Benign	21
DANN	Benign	0.94
DEOGEN2	Uncertain	0.45	T
Eigen	Benign	0.019
Eigen_PC	Benign	0.062
FATHMM_MKL	Uncertain	0.96	D
LIST_S2	Uncertain	0.95	D
M_CAP	Uncertain	0.22	D
MetaRNN	Uncertain	0.69	D
MetaSVM	Uncertain	-0.27	T
MutationAssessor	Benign	0.61	N
PhyloP100		6.1
PrimateAI	Pathogenic	0.82	D
PROVEAN	Benign	-1.8	N
REVEL	Pathogenic	0.68
Sift	Benign	0.63	T
Sift4G	Benign	0.63	T
Polyphen		0.98	D
Vest4		0.77
MutPred		0.64		Gain of glycosylation at Y218 (P = 0.0031)
MVP		0.91
MPC		1.6
ClinPred		0.95	D
GERP RS		4.3
Varity_R		0.69
gMVP		0.87
Mutation Taster		=3/97	disease causing (ClinVar)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs397514728; hg19: chr3-121980544;