C1QTNF2

C1q and TNF related 2, the group of C1q and TNF related

Basic information

Region (hg38): 5:160347754-160370641

Links

ENSG00000145861 ∙ NCBI:114898 ∙ OMIM:618647 ∙ HGNC:14325 ∙ Uniprot:Q9BXJ5 ∙ 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 C1QTNF2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C1QTNF2 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			39	1		40
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	39	1	0

Variants in C1QTNF2

This is a list of pathogenic ClinVar variants found in the C1QTNF2 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-160349176-C-T		not specified	Uncertain significance (Jan 26, 2022)
5-160349183-G-T		not specified	Uncertain significance (Apr 10, 2023)
5-160349189-C-G		not specified	Uncertain significance (Feb 15, 2023)
5-160349194-C-T		not specified	Uncertain significance (Dec 06, 2022)
5-160349244-T-C		not specified	Uncertain significance (Aug 17, 2022)
5-160349260-G-T		not specified	Uncertain significance (Mar 01, 2023)
5-160349295-C-T		not specified	Uncertain significance (Aug 08, 2022)
5-160349296-C-G		not specified	Uncertain significance (Sep 02, 2024)
5-160349332-C-T		not specified	Uncertain significance (Feb 28, 2023)
5-160349338-G-A		not specified	Uncertain significance (Apr 26, 2024)
5-160349364-C-T		not specified	Uncertain significance (Nov 19, 2022)
5-160349394-C-A		not specified	Uncertain significance (Oct 05, 2022)
5-160349398-T-C		not specified	Uncertain significance (Aug 12, 2021)
5-160349411-G-C		not specified	Uncertain significance (Mar 20, 2023)
5-160349421-G-A		not specified	Uncertain significance (Jan 27, 2025)
5-160349464-C-T		not specified	Uncertain significance (Dec 16, 2023)
5-160349500-C-T		not specified	Uncertain significance (Jan 16, 2024)
5-160349530-G-C		not specified	Uncertain significance (Oct 04, 2022)
5-160349611-C-T		not specified	Uncertain significance (Apr 06, 2022)
5-160349661-G-A		not specified	Uncertain significance (Dec 21, 2022)
5-160349671-T-C		not specified	Uncertain significance (Mar 15, 2024)
5-160349679-G-A		not specified	Uncertain significance (Jul 17, 2023)
5-160349713-C-T		not specified	Uncertain significance (Sep 21, 2021)
5-160349758-G-A		not specified	Uncertain significance (Feb 05, 2024)
5-160354786-C-T		not specified	Uncertain significance (May 14, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C1QTNF2	protein_coding	protein_coding	ENST00000393975	3	22891

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000835	0.799	125707	0	40	125747	0.000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.182	206	199	1.04	0.0000129	2084
Missense in Polyphen		68	64.996	1.0462		658
Synonymous	-0.159	90	88.1	1.02	0.00000629	716
Loss of Function	1.09	6	9.65	0.622	5.13e-7	118

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000310	0.000298
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000930	0.0000924
European (Non-Finnish)	0.000143	0.000141
Middle Eastern	0.00	0.00
South Asian	0.000397	0.000392
Other	0.000204	0.000163

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.144

Intolerance Scores

• loftool: 0.289
• rvis_EVS: -0.54
• rvis_percentile_EVS: 20.54

Haploinsufficiency Scores

• pHI: 0.165
• hipred: N
• hipred_score: 0.282
• ghis: 0.581

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.102

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: C1qtnf2
• Phenotype: skeleton phenotype

Gene ontology

• Biological process: activation of MAPK activity;positive regulation of glycogen biosynthetic process;positive regulation of fatty acid oxidation;positive regulation of glucose import;protein homooligomerization;protein heterotrimerization
• Cellular component: collagen trimer;extracellular space
• Molecular function: signaling receptor binding;protein binding;identical protein binding