CHERP

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

Basic information

Region (hg38): 19:16517894-16542437

Links

ENSG00000085872 ∙ NCBI:10523 ∙ OMIM:618539 ∙ HGNC:16930 ∙ Uniprot:Q8IWX8 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CHERP gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CHERP gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				4		4
missense			30	1		31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	30	5	0

Variants in CHERP

This is a list of pathogenic ClinVar variants found in the CHERP region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
19-16519284-C-T		not specified	Uncertain significance (Mar 07, 2024)
19-16519686-G-A		not specified	Uncertain significance (Jul 19, 2023)
19-16520170-C-T		not specified	Uncertain significance (Apr 21, 2022)
19-16520171-G-A		not specified	Uncertain significance (Oct 26, 2022)
19-16520233-C-T		not specified	Uncertain significance (Mar 25, 2024)
19-16520249-G-A		not specified	Uncertain significance (Oct 07, 2022)
19-16520377-G-A		not specified	Uncertain significance (Mar 15, 2024)
19-16520420-C-T			Likely benign (Oct 01, 2022)
19-16520424-C-T		not specified	Uncertain significance (Jan 30, 2024)
19-16520844-C-A		not specified	Uncertain significance (May 10, 2024)
19-16520850-C-T		not specified	Uncertain significance (Nov 14, 2023)
19-16523185-G-A		not specified	Uncertain significance (Jan 26, 2022)
19-16525269-C-T		not specified	Uncertain significance (Jan 18, 2023)
19-16525274-C-T		not specified	Uncertain significance (Mar 15, 2024)
19-16525286-G-A		not specified	Uncertain significance (Oct 06, 2022)
19-16525301-G-T		not specified	Uncertain significance (Aug 16, 2021)
19-16525364-T-A		not specified	Uncertain significance (Oct 25, 2022)
19-16525366-C-T			Likely benign (May 01, 2022)
19-16525376-T-C		not specified	Uncertain significance (Nov 21, 2023)
19-16525449-G-A		not specified	Uncertain significance (Jun 17, 2024)
19-16525581-C-T		not specified	Uncertain significance (Jul 14, 2022)
19-16528150-T-G		not specified	Uncertain significance (Jun 11, 2021)
19-16528151-C-T		not specified	Uncertain significance (Jul 13, 2022)
19-16528186-G-A		not specified	Uncertain significance (Feb 16, 2023)
19-16528200-T-A			Likely benign (Sep 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CHERP	protein_coding	protein_coding	ENST00000546361	17	24642

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	2.83e-8	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	4.25	285	570	0.500	0.0000383	5944
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in calcium homeostasis, growth and proliferation. {ECO:0000269|PubMed:10794731, ECO:0000269|PubMed:12656674}.
• Pathway: Spliceosome - Homo sapiens (human);Metabolism of RNA;mRNA Splicing - Major Pathway;mRNA Splicing;Processing of Capped Intron-Containing Pre-mRNA (Consensus)

Recessive Scores

• pRec: 0.117

Intolerance Scores

• loftool: 0.140
• rvis_EVS: -1.09
• rvis_percentile_EVS: 7.11

Haploinsufficiency Scores

• pHI: 0.249
• hipred: Y
• hipred_score: 0.853
• ghis: 0.656

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.917

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cherp

Gene ontology

• 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;positive regulation of calcineurin-NFAT signaling cascade
• Cellular component: nucleoplasm;cytoplasm;membrane;sarcoplasmic reticulum membrane;perinuclear region of cytoplasm
• Molecular function: RNA binding;protein binding;ion channel binding