C1QTNF3

C1q and TNF related 3, the group of C1q and TNF related

Basic information

Region (hg38): 5:34017857-34043213

Links

ENSG00000082196 ∙ NCBI:114899 ∙ OMIM:612045 ∙ HGNC:14326 ∙ Uniprot:Q9BXJ4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the C1QTNF3 gene.

• Inborn genetic diseases (7 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C1QTNF3 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense			7	1		8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	2	0

Variants in C1QTNF3

This is a list of pathogenic ClinVar variants found in the C1QTNF3 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
5-34020600-G-C		not specified	Uncertain significance (Feb 28, 2023)
5-34020627-G-A		not specified	Uncertain significance (Jan 08, 2024)
5-34023946-G-A		not specified	Uncertain significance (Dec 14, 2023)
5-34028802-C-G		not specified	Uncertain significance (Nov 02, 2023)
5-34028805-T-A		not specified	Uncertain significance (Aug 17, 2021)
5-34028842-C-A		not specified	Uncertain significance (Jul 19, 2023)
5-34035666-C-T			Likely benign (May 01, 2023)
5-34035667-G-A		not specified	Uncertain significance (Jan 04, 2024)
5-34035724-C-T		not specified	Uncertain significance (Aug 08, 2022)
5-34042870-G-A			Likely benign (May 01, 2023)
5-34042885-G-A		not specified	Uncertain significance (Dec 18, 2023)
5-34042933-T-G		not specified	Uncertain significance (Jan 03, 2022)
5-34042939-G-A		not specified	Uncertain significance (Nov 03, 2023)
5-34042975-C-T		not specified	Uncertain significance (Jun 22, 2023)
5-34042980-C-T		not specified	Uncertain significance (Aug 12, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C1QTNF3	protein_coding	protein_coding	ENST00000382065	6	24385

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.81e-7	0.434	125554	0	194	125748	0.000772

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.10	139	180	0.770	0.00000939	2118
Missense in Polyphen		57	72.352	0.78781		821
Synonymous	-0.355	73	69.2	1.05	0.00000377	612
Loss of Function	0.757	12	15.2	0.790	8.60e-7	160

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000385	0.000385
Ashkenazi Jewish	0.00407	0.00408
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000380	0.000378
Middle Eastern	0.000109	0.000109
South Asian	0.00310	0.00311
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.314

Intolerance Scores

• loftool: 0.434
• rvis_EVS: -0.07
• rvis_percentile_EVS: 48.12

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.139
• ghis: 0.531

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: C1qtnf3
• Phenotype: hematopoietic system phenotype; skeleton phenotype; immune system phenotype

Gene ontology

• Biological process: cellular triglyceride homeostasis;fat cell differentiation;negative regulation of gluconeogenesis;positive regulation of cytokine secretion;negative regulation of inflammatory response;positive regulation of adiponectin secretion;protein trimerization;negative regulation of monocyte chemotactic protein-1 production;negative regulation of interleukin-6 secretion;negative regulation of NIK/NF-kappaB signaling
• Cellular component: collagen trimer;cell;membrane;extracellular exosome
• Molecular function: molecular_function