C1QTNF9B

protein-coding

C1q and TNF related 9B, the group of C1q and TNF related

Gene summary

Predicted to enable hormone activity and identical protein binding activity. Predicted to act upstream of or within several processes, including negative regulation of cell size; positive regulation of cellular response to insulin stimulus; and positive regulation of protein serine/threonine kinase activity. Predicted to be located in obsolete extracellular space. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001007537.3

Inheritance

—

ClinVar variants

U:61B:8

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.93

Max pathogenic AF

—

Genomic locus

chr13:23,891,099-23,897,502

External References & Databases

Ensembl (ENSG00000205863)

Transcript & Mutation Effects

hg38 • Region Span ~6.4 kb

Loading mutation effect viewer...

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 C1QTNF9B variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 64

not providedTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001007537.3. 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			1 clinvar	1 clinvar	1 clinvar	3
missense			60 clinvar	4 clinvar	2 clinvar	66
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	61	5	3	69

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 6 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001007537.3	RefSeq	NP_001007538.1	3	MANE Select
ENST00000713589.1	Ensembl	ENSP00000518885.1	3	MANE Select
ENST00000382137.8	Ensembl	ENSP00000371572.3	3	Standard
ENST00000382145.5	Ensembl	ENSP00000371580.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

protein binding

Cellular Component

extracellular region
collagen trimer

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000382137
Coding exons: 3
Length: 11557
Individuals with no LoFs: 125523
Homozygous LoFs: 7
Heterozygous LoFs: 218
Defined: 125748
p: 0.000895

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.181	176	183	0.962	0.00000945	2090
Missense (PolyPhen)		76	75.137	1.0115		848
Synonymous	-0.118	76	74.7	1.02	0.00000439	683
Loss of Function	0.231	12	12.9	0.931	8.93e-7	135

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.00069	0.00064	rare
Ashkenazi Jewish	0.0049	0.0042	notable
East Asian	0.0032	0.0032	notable
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00039	0.00036	rare
South Asian	0.0018	0.0017	notable
Other	0.0012	0.0011	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Probable adipokine. Activates AMPK, AKT, and p44/42 MAPK signaling pathways. {ECO:0000250|UniProtKB:Q4ZJN1}.;

Intolerance Scores

RVIS EVS: 0.6
RVIS percentile EVS: 82.74

Essentials

Essential (CRISPR): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

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