CIPC

protein-coding

CLOCK interacting pacemaker

Gene summary

Predicted to be involved in negative regulation of DNA-templated transcription and negative regulation of circadian rhythm. Located in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

KIAA1737

MANE transcript

NM_033426.3

Inheritance

—

ClinVar variants

U:59B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.34

Max pathogenic AF

—

Genomic locus

chr14:77,098,126-77,117,287

External References & Databases

Ensembl (ENSG00000198894)

Transcript & Mutation Effects

hg38 • Region Span ~19.2 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 CIPC variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 61

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_033426.3. 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						0
missense			59 clinvar	2 clinvar		61
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	59	2	0	61

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 43 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_033426.3	RefSeq	NP_219494.2	3	MANE Select
ENST00000361786.7	Ensembl	ENSP00000355319.2	3	MANE Select
ENST00000554447.5	Ensembl	ENSP00000452380.1	3	Standard
ENST00000554658.5	Ensembl	ENSP00000451522.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

negative regulation of circadian rhythm
negative regulation of transcription, DNA-templated
rhythmic process

Molecular Function

protein binding

Cellular Component

nucleus
cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000361786
Coding exons: 3
Length: 19191
Individuals with no LoFs: 125732
Homozygous LoFs: 0
Heterozygous LoFs: 6
Defined: 125738
p: 0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.748	190	221	0.859	0.0000118	2579
Missense (PolyPhen)		56	78.618	0.71231		940
Synonymous	0.931	79	90.3	0.875	0.00000528	835
Loss of Function	2.10	4	11.8	0.340	4.99e-7	155

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	0.000054	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000044	0.000044	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Transcriptional repressor which may act as a negative- feedback regulator of CLOCK-ARNTL/BMAL1 transcriptional activity in the circadian-clock mechanism. May stimulate ARNTL/BMAL1- dependent phosphorylation of CLOCK. However, the physiogical relevance of these observations is unsure, since experiments in an animal model showed that CIPC is not critially required for basic circadian clock. {ECO:0000250|UniProtKB:Q8R0W1}.;

Intolerance Scores

RVIS EVS: -0.4
RVIS percentile EVS: 26.53

Essentials

Essential (gene trap): N

Gene Damage Prediction

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