chr3-122283764-G-A

Position:

• chr3-122283764-G-A

Variant summary

Our verdict is Pathogenic. Variant got 15 ACMG points: 15P and 0B. PM1 PM2 PP2 PP3_Moderate PP5_Very_Strong

The ENST00000639785.2(CASR):​c.1810G>A​(p.Glu604Lys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. 12/21 in silico tools predict a damaging outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E604A) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: CASR ENST00000639785.2 missense
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:9
• Conservation: PhyloP100: 10.0

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 hotspot region, there are 2 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 0 benign, 15 uncertain in ENST00000639785.2
• PM2: Very rare variant in population databases, with high coverage
• 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.
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.899
• PP5: Variant 3-122283764-G-A is Pathogenic according to our data. Variant chr3-122283764-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 8350.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-122283764-G-A is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CASR	NM_000388.4	c.1810G>A	p.Glu604Lys	missense_variant	7/7	ENST00000639785.2	NP_000379.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CASR	ENST00000639785.2	c.1810G>A	p.Glu604Lys	missense_variant	7/7	1	NM_000388.4	ENSP00000491584	P1
CASR	ENST00000498619.4	c.1840G>A	p.Glu614Lys	missense_variant	7/7	1		ENSP00000420194
CASR	ENST00000638421.1	c.1810G>A	p.Glu604Lys	missense_variant	7/7	5		ENSP00000492190	P1
CASR	ENST00000490131.7	c.1579G>A	p.Glu527Lys	missense_variant	5/5	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:3

Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Aug 25, 2015	The E604K missense variant in the CASR gene has been reported previously in autosomal dominant hypocalcemia (Tan et al., 2003; Alvarez-Hernández et al., 2003; Winer et al., 2014). E604K is a non-conservative amino acid substitution as a negatively charged Glutamic Acid residue is replaced with a positively charged Lysine residue. In vivo functional studies have shown that E604K is an activating variant, enhancing the receptor's extracellular calcium sensitivity (Tan et al., 2003). Therefore, we interpret E604K as a pathogenic variant. -
Pathogenic, criteria provided, single submitter	clinical testing	Athena Diagnostics	Jul 22, 2021	This variant has not been reported in large, multi-ethnic general populations (http://gnomad.broadinstitute.org). This variant appears to segregate with disease in at least one family. Assessment of experimental evidence suggests this variant results in abnormal protein function. This variant decreased the response of the receptor to calcium (PMID: 12574188). -
Pathogenic, criteria provided, single submitter	clinical testing	Genetic Services Laboratory, University of Chicago	Jun 22, 2020	DNA sequence analysis of the CASR gene demonstrated a sequence change, c.1810G>A, in exon 7 that results in an amino acid change, p.Glu604Lys. This sequence change has not been described in the large population databases such as ExAC and gnomAD (dbSNP rs104893712). This sequence change has previously been described in families with autosomal dominant hypocalcemia (PMID: 12574188) and hypoparathyroidism (PMIDs: 14519094,24948345). The p.Glu604Lys change affects a highly conserved amino acid residue located in a cysteine-rich domain of the extracellular head (PMID: 17039419, 14519094) and is classified as an activating mutation. Functional studies have suggested that this variant significantly increases the extracellular Ca2+ sensitivity of the receptor in vivo (PMID: 12574188). The p.Glu604Lys substitution appears to be deleterious using several in-silico pathogenicity prediction tools (SIFT, PolyPhen2, Align GVGD, REVEL). These collective evidences indicate that this sequence change is pathogenic. -

Autosomal dominant hypocalcemia 1 Pathogenic:2

Pathogenic, no assertion criteria provided	clinical testing	Bioscientia Institut fuer Medizinische Diagnostik GmbH, Sonic Healthcare	Jul 02, 2020	- -
Pathogenic, no assertion criteria provided	literature only	OMIM	Feb 01, 2003	- -

Nephrolithiasis/nephrocalcinosis Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Sep 11, 2023

The c.1810G>A (p.E604K) alteration is located in exon 7 (coding exon 6) of the CASR gene. This alteration results from a G to A substitution at nucleotide position 1810, causing the glutamic acid (E) at amino acid position 604 to be replaced by a lysine (K). Based on the available evidence, the CASR c.1810G>A (p.E604K) 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 (Ovejero, 2019; Winer, 2018; Hannan, 2012; Tan, 2003; Alvarez-Hernández, 2003). In addition, this variant has been determined to be the result of a de novo mutation in one individual with features consistent with CASR-related hypocalcemia (Qin, 2022). 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 (Tan, 2003; Cavaco, 2018). This alteration is predicted to be deleterious by in silico analysis. 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

Dec 19, 2023

The CASR c.1840G>A variant is predicted to result in the amino acid substitution p.Glu614Lys. This variant was reported to cause autosomal dominant hypocalcemia (reported as E604K in Tan et al. 2003. PubMed ID: 12574188; Hannan FM et al 2012. PubMed ID: 22422767). This variant was also reported in two patients with hypoparathyroidism (also reported as E604K in Patients G and H in Winer et al. 2014. PubMed ID: 24948345). In the Tan et al. study, this variant co-segregated with disease in a family, and functional studies showed that the p.Glu614Lys change enhances the extracellular Ca2+ sensitivity of the calcium-sensing receptor (CaR). This variant has not been reported in a large population database, indicating it 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

Sep 12, 2022

For these reasons, this variant has been classified as Pathogenic. Experimental studies have shown that this missense change affects CASR function (PMID: 12574188). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive. ClinVar contains an entry for this variant (Variation ID: 8350). This missense change has been observed in individual(s) with hypocalcemia and/or hypoparathyroidism (PMID: 12574188, 14519094, 24948345). 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 glutamic acid, which is acidic and polar, with lysine, which is basic and polar, at codon 604 of the CASR protein (p.Glu604Lys). -

Autosomal dominant hypocalcemia Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

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

Dec 01, 2021

Variant summary: CASR c.1810G>A (p.Glu604Lys) results in a non-conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant was absent in 251472 control chromosomes. c.1810G>A has been reported in the literature in multiple individuals affected with Autosomal Dominant Hypocalcemia, including 2 families where the variant segregated with the disease (Tan_2003, Alvarez-Hernandez_2003). These data indicate that the variant is very likely to be associated with disease. To our knowledge, least one publication reports experimental evidence evaluating an impact on protein function. The most pronounced variant effect results in approximately 60% of normal activity. Three ClinVar submitters have classified this variant (after 2014) as pathogenic . Based on the evidence outlined above, the variant was classified as pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.78
BayesDel_addAF	Pathogenic	0.46	D
BayesDel_noAF	Pathogenic	0.42
CADD	Pathogenic	26
DANN	Pathogenic	1.0
DEOGEN2	Pathogenic	0.81	D;D;.;.
Eigen	Pathogenic	0.97
Eigen_PC	Pathogenic	0.95
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Pathogenic	0.97	.;D;D;D
M_CAP	Pathogenic	0.54	D
MetaRNN	Pathogenic	0.90	D;D;D;D
MetaSVM	Pathogenic	0.90	D
MutationAssessor	Pathogenic	3.0	M;M;.;.
MutationTaster	Benign	1.0	A;A;A
PrimateAI	Pathogenic	0.84	D
PROVEAN	Uncertain	-3.8	.;.;D;.
REVEL	Pathogenic	0.81
Sift	Uncertain	0.0010	.;.;D;.
Sift4G	Uncertain	0.0040	.;.;D;.
Polyphen		1.0	D;D;.;.
Vest4		0.94
MutPred		0.68		.;.;Gain of methylation at E614 (P = 0.0109);.;
MVP		0.98
MPC		1.7
ClinPred		1.0	D
GERP RS		5.9
Varity_R		0.79
gMVP		0.98

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: rs104893712; hg19: chr3-122002611; COSMIC: COSV56134726;