C1QTNF6

protein-coding

C1q and TNF related 6, the group of C1q and TNF related

Gene summary

Enables identical protein binding activity. Predicted to be located in extracellular region. Predicted to be part of protein-containing complex. Predicted to be active in obsolete extracellular space. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_031910.4

Inheritance

—

ClinVar variants

U:52B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.92

Max pathogenic AF

—

Genomic locus

chr22:37,180,166-37,199,385

External References & Databases

Ensembl (ENSG00000133466)

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 C1QTNF6 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 55

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_031910.4. 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					2 clinvar	2
missense			52 clinvar	3 clinvar		55
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	52	3	2	57

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 18 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_031910.4	RefSeq	NP_114116.3	3	MANE Select
ENST00000337843.7	Ensembl	ENSP00000338812.2	3	MANE Select
NM_001365878.1	RefSeq	NP_001352807.1	2	Standard
NM_182486.2	RefSeq	NP_872292.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

protein heterotrimerization

Molecular Function

protein binding
identical protein binding

Cellular Component

collagen trimer
extracellular space

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000337843
Coding exons: 3
Length: 19219
Individuals with no LoFs: 125705
Homozygous LoFs: 0
Heterozygous LoFs: 40
Defined: 125745
p: 0.000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.513	168	188	0.895	0.0000122	1837
Missense (PolyPhen)		75	74.553	1.006		764
Synonymous	1.08	68	80.3	0.846	0.00000593	543
Loss of Function	0.212	8	8.67	0.922	3.70e-7	97

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00034	0.00031	rare
Latino/Admixed American	0.000087	0.000087	rare
Ashkenazi Jewish	0.00020	0.00020	rare
East Asian	0.00016	0.00016	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00011	0.00011	rare
South Asian	0.00043	0.00042	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.110

Intolerance Scores

LoFtool: 0.409
RVIS EVS: 1.06
RVIS percentile EVS: 91.58

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.570

Gene Damage Prediction

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