CAPS

protein-coding

calcyphosine, the group of EF-hand domain containing

Gene summary

This gene encodes a calcium-binding protein, which may play a role in the regulation of ion transport. A similar protein was first described as a potentially important regulatory protein in the dog thyroid and was termed as R2D5 antigen in rabbit. Alternative splicing of this gene generates two transcript variants. [provided by RefSeq, Jul 2008]

MANE transcript

NM_004058.5

Inheritance

—

ClinVar variants

U:54B:6

Top phenotype

CAPS-related disorder

gnomAD constraint

pLI —, LoF o/e 1.06

Max pathogenic AF

—

Genomic locus

chr19:5,912,339-5,916,211

External References & Databases

Ensembl (ENSG00000105519)

Transcript & Mutation Effects

hg38 • Region Span ~3.9 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CAPS variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 52

not providedTotal: 2

CAPS-related disorderTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_004058.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar		1
missense			52 clinvar	2 clinvar	3 clinvar	57
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	54	3	3	60

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 20 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_004058.5	RefSeq	NP_004049.3	4	MANE Select
ENST00000588776.8	Ensembl	ENSP00000465883.2	4	MANE Select
NM_080590.4	RefSeq	NP_542157.3	4	Standard
ENST00000452990.8	Ensembl	ENSP00000403263.3	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

intracellular signal transduction

Molecular Function

calcium ion binding

Cellular Component

cytoplasm
vesicle

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000222125
Coding exons: 4
Length: 4171
Individuals with no LoFs: 125642
Homozygous LoFs: 0
Heterozygous LoFs: 41
Defined: 125683
p: 0.000163

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.491	161	144	1.11	0.0000107	1223
Missense (PolyPhen)		53	52.646	1.0067		480
Synonymous	0.782	55	62.9	0.875	0.00000495	384
Loss of Function	-0.137	7	6.62	1.06	2.82e-7	72

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00068	0.00068	rare
Latino/Admixed American	0.00017	0.00017	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00016	0.00016	rare
South Asian	0.000098	0.000098	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Calcium-binding protein. May play a role in cellular signaling events (Potential). {ECO:0000305}.;

Intolerance Scores

LoFtool: 0.889
RVIS EVS: 0.46
RVIS percentile EVS: 78.69

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.273

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium