CARHSP1

protein-coding

calcium regulated heat stable protein 1

Gene summary

Enables mRNA 3'-UTR binding activity. Predicted to be involved in regulation of mRNA stability. Predicted to be located in P granule; cytoplasmic exosome (RNase complex); and cytosol. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_014316.4

Inheritance

—

ClinVar variants

U:53B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.17

Max pathogenic AF

—

Genomic locus

chr16:8,852,942-8,869,012

External References & Databases

Ensembl (ENSG00000153048)

Transcript & Mutation Effects

hg38 • Region Span ~16.1 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 CARHSP1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 50

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_014316.4. 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 clinvar		2
missense			50 clinvar			50
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	53	1	0	54

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 164 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_014316.4	RefSeq	NP_055131.2	3	MANE Select
ENST00000311052.10	Ensembl	ENSP00000311847.4	3	MANE Select
NM_001042476.2	RefSeq	NP_001035941.1	3	Standard
NM_001278260.2	RefSeq	NP_001265189.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

miR-targeted genes in lymphocytes - TarBase
miR-targeted genes in muscle cell - TarBase

Biological Process

regulation of transcription by RNA polymerase II
intracellular signal transduction
regulation of mRNA stability

Molecular Function

DNA-binding transcription factor activity, RNA polymerase II-specific
DNA binding
mRNA 3'-UTR binding
protein binding
phosphatase binding

Cellular Component

cytoplasmic exosome (RNase complex)
P-body
cytoplasm
cytosol
P granule

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000396593
Coding exons: 3
Length: 16068
Individuals with no LoFs: 125716
Homozygous LoFs: 0
Heterozygous LoFs: 27
Defined: 125743
p: 0.000107

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-2.38	160	94.8	1.69	0.00000629	907
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000064	0.000062	rare
Latino/Admixed American	0.00015	0.00014	rare
Ashkenazi Jewish	0.00012	0.000099	rare
East Asian	0.00012	0.00011	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00010	0.000097	rare
South Asian	0.00020	0.00020	rare
Other	0.00019	0.00016	rare

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.115

Intolerance Scores

LoFtool: 0.134
RVIS EVS: -0.78
RVIS percentile EVS: 12.77

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.997

Gene Damage Prediction

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