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.

• not_specified (71 variants)

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. These statistics are base on transcript: NM_000031909.3. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			70	1		71
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	70	1	0

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