3-122284197-C-G

Position:

• chr3-122284197-C-G

Variant summary

Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PM1 PM2 PM5 PP2 PP3_Strong PP5

The NM_000388.4(CASR):​c.2243C>G​(p.Pro748Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,402 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P748L) has been classified as Pathogenic.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000014 (0 hom.)
• Consequence: CASR NM_000388.4 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:3 U:1
• Conservation: PhyloP100: 7.90

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.

• PM1: In a topological_domain Extracellular (size 23) in uniprot entity CASR_HUMAN there are 9 pathogenic changes around while only 1 benign (90%) 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 chr3-122284197-C-T is described in Lovd as [Pathogenic].
• 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, 0.993
• PP5: Variant 3-122284197-C-G is Pathogenic according to our data. Variant chr3-122284197-C-G is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 936871.We mark this variant Likely_pathogenic, oryginal submissions are: {Uncertain_significance=1, Pathogenic=2, Likely_pathogenic=1}. Variant chr3-122284197-C-G is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CASR	NM_000388.4	c.2243C>G	p.Pro748Arg	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.2243C>G	p.Pro748Arg	missense_variant	7/7	1	NM_000388.4	ENSP00000491584.2
CASR	ENST00000498619.4	c.2273C>G	p.Pro758Arg	missense_variant	7/7	1		ENSP00000420194.1
CASR	ENST00000638421.1	c.2243C>G	p.Pro748Arg	missense_variant	7/7	5		ENSP00000492190.1
CASR	ENST00000490131.7	c.2012C>G	p.Pro671Arg	missense_variant	5/5	5		ENSP00000418685.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000137 AC: 2 AN: 1461402 Hom.: 0 Cov.: 33 AF XY: 0.00000138 AC XY: 1 AN XY: 727016

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000180

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:3 Uncertain:1

Revision: criteria provided, conflicting classifications

Submissions by phenotype

Familial hypocalciuric hypercalcemia 1 Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Genetics and Molecular Pathology, SA Pathology

Jul 19, 2023

The CASR c.2243C>G variant is classified as Pathogenic (PS4_Moderate, PS3, PM2, PP3, PP1_Moderate) The CASR c.2243C>G variant is a single nucleotide change in exon 7/7 of the CASR gene, which is predicted to change the amino acid proline at position 748 in the protein to arginine. This variant is absent from population databases (PM2). It has been reported in the literature to segregate with disease in a family affected by FHH (PMID: 8636323) (PP1_Moderate) and has been detected in two unrelated individuals affected by FHH and PHPT (PMID: 22232026, 3237971) (PS4_Moderate). Functional studies suggest a detrimental effect on CASR protein function (PMID: 19389809, PMID: 22798347) and has been shown to alter binding affinity of allosteric modulators (PMID: 23372019) (PS3). Two other missense changes at codon 748 have also been reported in the literature in association with FHH (PMID: 19073830, 22422767). Computational predictions (REVEL = 0.951) support a deleterious effect on the gene or gene product (PP3). The variant has been reported in dbSNP (rs193922433) and in the HGMD database: CM962443. It has been reported as VUS and Likely pathogenic by other diagnostic laboratories (ClinVar Variation ID: 936871). -

not provided Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Athena Diagnostics

Dec 30, 2019

Not found in the total gnomAD dataset, and the data is high quality. Found in at least one patient with expected phenotype for this gene. Predicted to have a damaging effect on the protein. Assessment of experimental evidence suggests this variant results in abnormal protein function. -

Familial hypocalciuric hypercalcemia Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

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

Jul 24, 2023

Variant summary: CASR c.2243C>G (p.Pro748Arg) results in a non-conservative amino acid change located in the GPCR family 3, C-terminal domain (IPR017978) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant was absent in 250768 control chromosomes. c.2243C>G has been reported in the literature in multiple individuals affected with Familial Hypocalciuric Hypercalcemia (example, Heath_1996, Hannan_2012, Eldeiry_2012, Vargas-Poussou_2016, Arshad_2021) at-least one of these reports included an individual affected with Familial Hypocalciuric Hypercalcemia (FHH) and Primary Hyperparathyroidism (Eldeiry_2012). These data indicate that the variant is very likely to be associated with disease. At least one publication reports experimental evidence evaluating an impact on protein function (example, White__2009). The most pronounced variant effect results in impaired localization to plasma membrane and not trafficked to Golgi. The following publications have been ascertained in the context of this evaluation (PMID: 32892159, 22232026, 22422767, 8636323, 11013439, 17979873, 23372019, 11762699, 26963950, 19389809). Three submitters have cited clinical-significance assessments for this variant to ClinVar after 2014 (LP, n=2; VUS, n=1). Based on the evidence outlined above, the variant was classified as pathogenic. -

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

Uncertain significance, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Sep 09, 2019

This sequence change replaces proline with arginine at codon 748 of the CASR protein (p.Pro748Arg). The proline residue is highly conserved and there is a moderate physicochemical difference between proline and arginine. This variant is not present in population databases (ExAC no frequency). This variant has been observed in several families affected with familial hypocalciuric hypercalcemia and to segregate with disease in a family (PMID: 8636323, 26963950). This variant has also been observed in an individual affected with familial hypocalciuric hypercalcemia and primary hyperparathyroidism (PMID: 22232026). This variant has been reported to affect CASR protein function (PMID: 19389809, 22798347, 23372019). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.98
BayesDel_addAF	Pathogenic	0.47	D
BayesDel_noAF	Pathogenic	0.44
CADD	Pathogenic	27
DANN	Uncertain	1.0
DEOGEN2	Pathogenic	0.91	D;D;.;.
Eigen	Pathogenic	1.0
Eigen_PC	Pathogenic	0.96
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Uncertain	0.97	.;D;D;D
M_CAP	Pathogenic	0.68	D
MetaRNN	Pathogenic	0.99	D;D;D;D
MetaSVM	Pathogenic	1.0	D
MutationAssessor	Pathogenic	3.2	M;M;.;.
PrimateAI	Uncertain	0.78	T
PROVEAN	Pathogenic	-8.3	.;.;D;.
REVEL	Pathogenic	0.95
Sift	Pathogenic	0.0	.;.;D;.
Sift4G	Pathogenic	0.0010	.;.;D;.
Polyphen		1.0	D;D;.;.
Vest4		0.92
MutPred		0.94		.;.;Loss of catalytic residue at P757 (P = 0.0101);.;
MVP		1.0
MPC		1.6
ClinPred		1.0	D
GERP RS		5.9
Varity_R		0.93
gMVP		0.95

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: rs193922433; hg19: chr3-122003044;