C1QTNF6

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

Basic information

Region (hg38): 22:37180166-37199385

Links

ENSG00000133466 ∙ NCBI:114904 ∙ OMIM:614910 ∙ HGNC:14343 ∙ Uniprot:Q9BXI9 ∙ 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 C1QTNF6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C1QTNF6 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					2	2
missense			19	1		20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	1	2

Variants in C1QTNF6

This is a list of pathogenic ClinVar variants found in the C1QTNF6 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-37182193-C-T		not specified	Uncertain significance (Jul 21, 2021)
22-37182268-G-A		not specified	Uncertain significance (Feb 22, 2023)
22-37182340-T-C		not specified	Uncertain significance (Aug 13, 2021)
22-37182349-G-A		not specified	Uncertain significance (Apr 19, 2024)
22-37182352-C-T		not specified	Uncertain significance (Feb 13, 2024)
22-37182379-C-T		not specified	Uncertain significance (Jun 02, 2023)
22-37182429-C-T		not specified	Uncertain significance (Dec 14, 2023)
22-37182439-T-G		not specified	Uncertain significance (May 02, 2024)
22-37182462-C-T		not specified	Uncertain significance (Nov 08, 2022)
22-37182484-C-T		not specified	Uncertain significance (Dec 11, 2023)
22-37182528-T-C		not specified	Uncertain significance (Feb 05, 2024)
22-37182537-A-G		not specified	Uncertain significance (May 17, 2023)
22-37182553-C-T		not specified	Uncertain significance (May 24, 2023)
22-37182576-C-T		not specified	Uncertain significance (Mar 19, 2024)
22-37182600-C-T		not specified	Uncertain significance (Mar 15, 2024)
22-37182616-C-T		not specified	Uncertain significance (Feb 02, 2022)
22-37182687-C-T		not specified	Likely benign (Jun 26, 2023)
22-37182696-T-A		not specified	Uncertain significance (Jul 25, 2023)
22-37185231-G-A			Benign (Nov 13, 2018)
22-37185239-T-C		not specified	Uncertain significance (Jul 13, 2021)
22-37185315-G-T		not specified	Uncertain significance (Jun 10, 2022)
22-37185344-C-T		not specified	Uncertain significance (Jan 22, 2024)
22-37185380-T-C		not specified	Uncertain significance (Feb 27, 2023)
22-37185383-G-T		not specified	Uncertain significance (Mar 20, 2024)
22-37185393-C-A		not specified	Uncertain significance (Dec 13, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C1QTNF6	protein_coding	protein_coding	ENST00000337843	3	19219

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000901	0.337	125705	0	40	125745	0.000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.513	168	188	0.895	0.0000122	1837
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000431	0.000394
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.000163	0.000163
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.000106	0.000105
Middle Eastern	0.000163	0.000163
South Asian	0.000426	0.000425
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.110

Intolerance Scores

• loftool: 0.409
• rvis_EVS: 1.06
• rvis_percentile_EVS: 91.58

Haploinsufficiency Scores

• pHI: 0.161
• hipred: N
• hipred_score: 0.146
• ghis: 0.403

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.570

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: C1qtnf6

Gene ontology

• Biological process: protein heterotrimerization
• Cellular component: collagen trimer;extracellular space
• Molecular function: protein binding;identical protein binding