C1QTNF4

protein-coding

C1q and TNF related 4, the group of C1q and TNF related

Gene summary

Predicted to enable cytokine activity. Involved in positive regulation of cytokine production and positive regulation of signal transduction. Located in obsolete extracellular space. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_031909.3

Inheritance

—

ClinVar variants

U:81B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.32

Max pathogenic AF

—

Genomic locus

chr11:47,589,667-47,594,411

External References & Databases

Ensembl (ENSG00000172247)

Transcript & Mutation Effects

hg38 • Region Span ~4.7 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 C1QTNF4 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 82

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_031909.3. 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			81 clinvar	1 clinvar		82
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	81	1	0	82

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 8 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_031909.3	RefSeq	NP_114115.2	1	MANE Select
ENST00000302514.4	Ensembl	ENSP00000302274.3	1	MANE Select
ENST00000530097.1	Ensembl	ENSP00000434548.1	2	Standard
ENST00000862513.1	Ensembl	ENSP00000532572.1	1	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

regulation of signaling receptor activity
positive regulation of interleukin-6 production
positive regulation of interleukin-6-mediated signaling pathway
positive regulation of NIK/NF-kappaB signaling
positive regulation of tumor necrosis factor secretion

Molecular Function

molecular_function
cytokine activity

Cellular Component

extracellular space

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000302514
Coding exons: 1
Length: 4996
Individuals with no LoFs: 124219
Homozygous LoFs: 0
Heterozygous LoFs: 8
Defined: 124227
p: 0.0000322

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.65	139	205	0.677	0.0000152	1999
Missense (PolyPhen)		23	55.182	0.4168		526
Synonymous	1.14	95	110	0.862	0.00000975	720
Loss of Function	1.60	2	6.35	0.315	3.52e-7	65

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000030	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000060	0.000054	rare
South Asian	0.000034	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May act as a pro-inflammatory cytokine, that induces the activation of NF-kappa-B signaling pathway and up-regulates IL6 production. {ECO:0000269|PubMed:21658842}.;

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.249

Gene Damage Prediction

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