CARHSP1

calcium regulated heat stable protein 1

Basic information

Region (hg38): 16:8852941-8869012

Links

ENSG00000153048 ∙ NCBI:23589 ∙ OMIM:616885 ∙ HGNC:17150 ∙ Uniprot:Q9Y2V2 ∙ 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 CARHSP1 gene.

• Inborn genetic diseases (17 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CARHSP1 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				1		1
missense			17			17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	1	0

Variants in CARHSP1

This is a list of pathogenic ClinVar variants found in the CARHSP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-8855200-C-G		not specified	Uncertain significance (Mar 06, 2023)
16-8855270-G-A		not specified	Uncertain significance (Jul 19, 2022)
16-8855303-A-G		not specified	Uncertain significance (May 05, 2023)
16-8858372-C-G		not specified	Uncertain significance (Jan 24, 2024)
16-8858378-C-T		not specified	Uncertain significance (Dec 15, 2023)
16-8858383-T-A		not specified	Uncertain significance (Apr 13, 2022)
16-8858383-T-G		not specified	Uncertain significance (Feb 02, 2024)
16-8858392-G-T		not specified	Uncertain significance (Jun 06, 2023)
16-8858447-C-A		not specified	Uncertain significance (Apr 20, 2023)
16-8858455-T-C		not specified	Uncertain significance (Aug 10, 2023)
16-8858464-C-A		not specified	Uncertain significance (Jun 06, 2023)
16-8858470-G-A		not specified	Uncertain significance (Feb 01, 2023)
16-8859174-G-A		not specified	Uncertain significance (Jun 21, 2022)
16-8859179-G-C			Likely benign (Mar 01, 2023)
16-8859199-G-C		not specified	Uncertain significance (Sep 22, 2023)
16-8859217-C-T		not specified	Uncertain significance (Mar 01, 2023)
16-8859225-C-T		not specified	Uncertain significance (Nov 28, 2023)
16-8859243-C-G		not specified	Uncertain significance (Oct 05, 2023)
16-8859243-C-T		not specified	Uncertain significance (Jun 21, 2023)
16-8859250-G-A		not specified	Uncertain significance (Dec 22, 2023)
16-8859252-C-T		not specified	Uncertain significance (May 25, 2022)
16-8859255-C-T		not specified	Uncertain significance (Mar 22, 2023)
16-8859256-G-C		not specified	Uncertain significance (Sep 12, 2023)
16-8859261-G-C		not specified	Uncertain significance (Jun 29, 2023)
16-8859286-G-C		not specified	Uncertain significance (Feb 05, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CARHSP1	protein_coding	protein_coding	ENST00000396593	3	16068

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000503	0.261	125716	0	27	125743	0.000107

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-2.38	160	94.8	1.69	0.00000629	907
Missense in Polyphen		37	29.598	1.2501		301
Synonymous	-5.94	86	38.9	2.21	0.00000248	318
Loss of Function	-0.355	6	5.13	1.17	3.03e-7	61

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000213	0.000210
Ashkenazi Jewish	0.000119	0.0000992
East Asian	0.000117	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000102	0.0000967
Middle Eastern	0.000117	0.000109
South Asian	0.000202	0.000196
Other	0.000194	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds mRNA and regulates the stability of target mRNA. Binds single-stranded DNA (in vitro). {ECO:0000269|PubMed:21078874, ECO:0000269|PubMed:21177848}.
• Pathway: miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase (Consensus)

Recessive Scores

• pRec: 0.115

Intolerance Scores

• loftool: 0.134
• rvis_EVS: -0.78
• rvis_percentile_EVS: 12.77

Haploinsufficiency Scores

• pHI: 0.414
• ghis: 0.634

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.997

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Carhsp1

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;intracellular signal transduction;regulation of mRNA stability
• Cellular component: cytoplasmic exosome (RNase complex);P-body;cytoplasm;cytosol;P granule
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;mRNA 3'-UTR binding;protein binding;phosphatase binding