CHERP

protein-coding

calcium homeostasis endoplasmic reticulum protein, the group of G-patch domain containing|Spliceosomal A complex

Gene summary

Enables transmembrane transporter binding activity. Involved in positive regulation of calcineurin-NFAT signaling cascade and release of sequestered calcium ion into cytosol. Acts upstream of or within intracellular calcium ion homeostasis and negative regulation of cell population proliferation. Located in perinuclear region of cytoplasm. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_006387.6

Inheritance

—

ClinVar variants

U:108B:7

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chr19:16,517,894-16,542,437

External References & Databases

Ensembl (ENSG00000085872)

Transcript & Mutation Effects

hg38 • Region Span ~24.5 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 CHERP variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 99

not providedTotal: 5

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_006387.6. 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			2 clinvar	5 clinvar		7
missense			101 clinvar	2 clinvar		103
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	108	7	0	115

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 35 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_006387.6	RefSeq	NP_006378.3	17	MANE Select
ENST00000546361.7	Ensembl	ENSP00000439856.2	17	MANE Select
ENST00000198939.6	Ensembl	ENSP00000198939.6	17	Standard
ENST00000198939.7	Ensembl	ENSP00000198939.6	17	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Spliceosome - Homo sapiens (human)
Metabolism of RNA
mRNA Splicing - Major Pathway
mRNA Splicing
Processing of Capped Intron-Containing Pre-mRNA

Biological Process

mRNA splicing, via spliceosome
cellular calcium ion homeostasis
nervous system development
negative regulation of cell population proliferation
release of sequestered calcium ion into cytosol

Molecular Function

RNA binding
protein binding
ion channel binding

Cellular Component

nucleoplasm
cytoplasm
membrane
sarcoplasmic reticulum membrane
perinuclear region of cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000546361
Coding exons: 17
Length: 24642
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	4.25	285	570	0.500	0.0000383	5944
Missense (PolyPhen)		83	182.24	0.45544		1991
Synonymous	-0.0101	242	242	1.00	0.0000180	1739
Loss of Function	6.42	0	48.0	0.00	0.00000241	492

Population LoF Frequency

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

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Involved in calcium homeostasis, growth and proliferation. {ECO:0000269|PubMed:10794731, ECO:0000269|PubMed:12656674}.;

Recessive Scores

pRec: 0.117

Intolerance Scores

LoFtool: 0.140
RVIS EVS: -1.09
RVIS percentile EVS: 7.11

Essentials

Essential (CRISPR): N
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.917

Gene Damage Prediction

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