C1QTNF1

C1q and TNF related 1, the group of C1q and TNF related

Basic information

Region (hg38): 17:79022814-79049788

Links

ENSG00000173918 ∙ NCBI:114897 ∙ OMIM:610365 ∙ HGNC:14324 ∙ Uniprot:Q9BXJ1 ∙ 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 C1QTNF1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C1QTNF1 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	2
missense			26			26
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	27	1	1

Variants in C1QTNF1

This is a list of pathogenic ClinVar variants found in the C1QTNF1 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-79044000-C-T		not specified	Uncertain significance (Nov 09, 2024)
17-79044024-C-T		not specified	Uncertain significance (Mar 29, 2023)
17-79044044-C-T		not specified	Uncertain significance (Mar 01, 2023)
17-79044045-G-A		not specified	Uncertain significance (Sep 01, 2021)
17-79044067-A-T		not specified	Uncertain significance (Oct 20, 2024)
17-79044093-A-T		not specified	Uncertain significance (Jul 25, 2024)
17-79044102-C-T		not specified	Uncertain significance (Nov 29, 2021)
17-79044119-G-A		not specified	Uncertain significance (Jun 22, 2021)
17-79046592-G-C		not specified	Uncertain significance (Jul 19, 2022)
17-79046613-C-T		not specified	Uncertain significance (Jan 30, 2024)
17-79046623-G-A		not specified	Uncertain significance (Oct 29, 2024)
17-79046647-T-C		not specified	Uncertain significance (Feb 13, 2025)
17-79046653-C-T		not specified	Uncertain significance (Oct 09, 2024)
17-79046655-G-C		not specified	Uncertain significance (Jun 11, 2021)
17-79046661-G-A		not specified	Uncertain significance (Jan 04, 2022)
17-79047540-G-A		not specified	Uncertain significance (Oct 10, 2023)
17-79047552-C-G		not specified	Uncertain significance (Jan 26, 2023)
17-79047553-G-A		not specified	Uncertain significance (Oct 19, 2021)
17-79047616-C-T		not specified	Uncertain significance (Dec 21, 2022)
17-79047669-A-G		not specified	Uncertain significance (Mar 31, 2023)
17-79047677-C-T			Benign (Apr 10, 2018)
17-79047724-A-G		not specified	Uncertain significance (Nov 24, 2024)
17-79047733-C-G		not specified	Uncertain significance (Nov 24, 2024)
17-79047733-C-T		not specified	Uncertain significance (Jun 18, 2021)
17-79047743-C-T			Likely benign (Jun 22, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C1QTNF1	protein_coding	protein_coding	ENST00000339142	3	26975

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000424	0.869	125725	0	23	125748	0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.525	167	187	0.892	0.0000122	1841
Missense in Polyphen		59	73.514	0.80257		738
Synonymous	0.385	77	81.4	0.946	0.00000598	540
Loss of Function	1.34	7	12.0	0.582	5.99e-7	128

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000231	0.000231
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000107	0.000105
Middle Eastern	0.000109	0.000109
South Asian	0.0000336	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.120

Intolerance Scores

• loftool: 0.499
• rvis_EVS: -0.36
• rvis_percentile_EVS: 29.16

Haploinsufficiency Scores

• pHI: 0.346
• hipred: Y
• hipred_score: 0.662
• ghis: 0.545

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.881

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: C1qtnf1
• Phenotype: adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; homeostasis/metabolism phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); liver/biliary system phenotype

Gene ontology

• Biological process: positive regulation of cytosolic calcium ion concentration;negative regulation of platelet activation;positive regulation of gene expression;regulation of glucose metabolic process;positive regulation of MAPK cascade;protein homooligomerization;positive regulation of protein kinase B signaling;protein heterotrimerization;negative regulation of platelet aggregation;positive regulation of aldosterone secretion
• Cellular component: collagen trimer;extracellular space;integral component of plasma membrane
• Molecular function: protein binding;collagen binding