C1QTNF4

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

Basic information

Region (hg38): 11:47589667-47594411

Links

ENSG00000172247 ∙ NCBI:114900 ∙ OMIM:614911 ∙ HGNC:14346 ∙ Uniprot:Q9BXJ3 ∙ 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 C1QTNF4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C1QTNF4 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						0
missense			47			47
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	47	0	0

Variants in C1QTNF4

This is a list of pathogenic ClinVar variants found in the C1QTNF4 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-47589846-C-A		not specified	Uncertain significance (Jul 06, 2021)
11-47589847-C-A		not specified	Uncertain significance (Mar 19, 2024)
11-47589927-C-T		not specified	Uncertain significance (Sep 07, 2022)
11-47589970-C-T		not specified	Uncertain significance (Jan 26, 2025)
11-47590009-C-T		not specified	Uncertain significance (May 15, 2024)
11-47590020-G-A		not specified	Uncertain significance (Apr 19, 2024)
11-47590073-C-A		not specified	Uncertain significance (Oct 21, 2024)
11-47590120-A-C		not specified	Uncertain significance (Jun 13, 2024)
11-47590123-A-G		not specified	Uncertain significance (Jun 13, 2024)
11-47590140-C-T		not specified	Uncertain significance (Nov 11, 2024)
11-47590167-T-G		not specified	Uncertain significance (Jul 20, 2021)
11-47590168-C-T		not specified	Uncertain significance (Oct 07, 2024)
11-47590222-G-A		not specified	Uncertain significance (May 12, 2024)
11-47590227-C-A		not specified	Uncertain significance (May 27, 2022)
11-47590258-G-C		not specified	Uncertain significance (Aug 17, 2021)
11-47590285-G-A		not specified	Uncertain significance (Apr 18, 2023)
11-47590288-G-T		not specified	Uncertain significance (Jun 06, 2022)
11-47590293-G-T		not specified	Uncertain significance (Jan 10, 2023)
11-47590297-G-C		not specified	Uncertain significance (Sep 27, 2021)
11-47590314-G-C		not specified	Uncertain significance (Nov 27, 2023)
11-47590318-G-A		not specified	Uncertain significance (May 10, 2024)
11-47590336-C-T		not specified	Uncertain significance (Oct 17, 2024)
11-47590339-C-G		not specified	Uncertain significance (Jun 26, 2024)
11-47590342-A-C		not specified	Uncertain significance (Dec 23, 2024)
11-47590362-G-A		not specified	Uncertain significance (Mar 21, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C1QTNF4	protein_coding	protein_coding	ENST00000302514	1	4996

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.172	0.775	124219	0	8	124227	0.0000322

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.65	139	205	0.677	0.0000152	1999
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000305	0.0000305
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000603	0.0000537
Middle Eastern	0.00	0.00
South Asian	0.0000338	0.0000327
Other	0.00	0.00

dbNSFP

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}.

Haploinsufficiency Scores

• pHI: 0.0938
• hipred: Y
• hipred_score: 0.559
• ghis: 0.516

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.249

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: C1qtnf4
• Phenotype: normal phenotype

Gene ontology

• 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;positive regulation of interleukin-6 secretion
• Cellular component: extracellular space
• Molecular function: molecular_function;cytokine activity