3-122261697-C-T

Position:

• chr3-122261697-C-T

Variant summary

Our verdict is Pathogenic. Variant got 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 Likely pathogenic.

• Frequency: Genomes: not found (cov: 32)
• Consequence: CASR NM_000388.4 missense
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:9
• Conservation: PhyloP100: 6.14

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 15 ACMG points.

• PM1: In a helix (size 13) in uniprot entity CASR_HUMAN there are 15 pathogenic changes around while only 0 benign (100%) 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 chrnull-null-null-null is described in UniProt as null.
• PP2: Missense variant in gene, where missense usually causes diseases (based on misZ statistic), CASR. . Gene score misZ 3.1237 (greater than the threshold 3.09). Trascript score misZ 4.8257 (greater than threshold 3.09). GenCC has associacion of gene with epilepsy, autosomal dominant hypocalcemia, familial hypocalciuric hypercalcemia 1, epilepsy, idiopathic generalized, susceptibility to, 8, neonatal severe primary hyperparathyroidism, autosomal dominant hypocalcemia 1.
• PP5: Variant 3-122261697-C-T is Pathogenic according to our data. Variant chr3-122261697-C-T is described in ClinVar as [Pathogenic]. Clinvar id is 60667.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-122261697-C-T is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CASR	NM_000388.4	c.662C>T	p.Pro221Leu	missense_variant	4/7	ENST00000639785.2	NP_000379.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CASR	ENST00000639785.2	c.662C>T	p.Pro221Leu	missense_variant	4/7	1	NM_000388.4	ENSP00000491584	P1
CASR	ENST00000498619.4	c.662C>T	p.Pro221Leu	missense_variant	4/7	1		ENSP00000420194
CASR	ENST00000638421.1	c.662C>T	p.Pro221Leu	missense_variant	4/7	5		ENSP00000492190	P1
CASR	ENST00000490131.7	c.662C>T	p.Pro221Leu	missense_variant	3/5	5		ENSP00000418685

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:9

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Athena Diagnostics	Jan 14, 2015	- -
Pathogenic, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Apr 01, 2021	- -

Autosomal dominant hypocalcemia Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Nov 12, 2021	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. -
Pathogenic, criteria provided, single submitter	clinical testing	Molecular Genetics, Royal Melbourne Hospital	Sep 05, 2022	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. -

Autosomal dominant hypocalcemia 1 Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

OMIM

Jun 15, 2012

- -

Nephrolithiasis/nephrocalcinosis Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Sep 12, 2023

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

Pathogenic, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Jan 31, 2024

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

Pathogenic, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jun 23, 2023

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. ClinVar contains an entry for this variant (Variation ID: 60667). This variant is also known as 1034C>T. 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 not present in population databases (gnomAD no frequency). 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). 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

Pathogenic, criteria provided, single submitter

clinical testing

Fulgent Genetics, Fulgent Genetics

Oct 23, 2021

- -

Computational scores

Source: dbNSFP v4.3

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;T;.;.
Eigen	Benign	0.019
Eigen_PC	Benign	0.062
FATHMM_MKL	Uncertain	0.96	D
LIST_S2	Uncertain	0.95	.;D;D;D
M_CAP	Uncertain	0.22	D
MetaRNN	Uncertain	0.69	D;D;D;D
MetaSVM	Uncertain	-0.27	T
MutationAssessor	Benign	0.61	N;N;N;.
MutationTaster	Benign	1.0	D;D;D
PrimateAI	Pathogenic	0.82	D
PROVEAN	Benign	-1.8	.;.;N;N
REVEL	Pathogenic	0.68
Sift	Benign	0.63	.;.;T;T
Sift4G	Benign	0.63	.;.;T;T
Polyphen		0.98	D;D;.;.
Vest4		0.77, 0.79
MutPred		0.64		Gain of glycosylation at Y218 (P = 0.0031);Gain of glycosylation at Y218 (P = 0.0031);Gain of glycosylation at Y218 (P = 0.0031);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

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

Publications

LitVar

Other links and lift over

dbSNP: rs397514728; hg19: chr3-121980544;