C1QL4

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

Basic information

Region (hg38): 12:49332409-49337188

Links

ENSG00000186897 ∙ NCBI:338761 ∙ OMIM:615229 ∙ HGNC:31416 ∙ Uniprot:Q86Z23 ∙ 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 C1QL4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C1QL4 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			30	1		31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	30	1	0

Variants in C1QL4

This is a list of pathogenic ClinVar variants found in the C1QL4 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-49333137-T-C		not specified	Uncertain significance (Oct 16, 2024)
12-49333226-G-T		not specified	Uncertain significance (Jul 12, 2023)
12-49335978-C-G		not specified	Uncertain significance (Aug 12, 2021)
12-49335988-C-A		not specified	Uncertain significance (Oct 29, 2024)
12-49335988-C-T		not specified	Uncertain significance (Jun 04, 2024)
12-49336021-C-T		not specified	Uncertain significance (Apr 26, 2024)
12-49336033-G-A		not specified	Uncertain significance (Dec 19, 2023)
12-49336056-G-T		not specified	Uncertain significance (Mar 18, 2024)
12-49336083-A-C		not specified	Uncertain significance (Jan 06, 2023)
12-49336114-C-T		not specified	Uncertain significance (Nov 11, 2024)
12-49336115-C-G		not specified	Uncertain significance (Jul 05, 2024)
12-49336137-G-C		not specified	Uncertain significance (Dec 18, 2023)
12-49336153-G-A		not specified	Uncertain significance (Dec 06, 2024)
12-49336180-C-G		not specified	Uncertain significance (Nov 18, 2022)
12-49336189-G-A		not specified	Uncertain significance (Nov 21, 2022)
12-49336209-G-T		not specified	Uncertain significance (Dec 24, 2024)
12-49336213-G-C		not specified	Uncertain significance (Dec 16, 2021)
12-49336215-C-A		not specified	Uncertain significance (Oct 20, 2024)
12-49336225-C-G		not specified	Uncertain significance (May 26, 2024)
12-49336239-G-T		not specified	Uncertain significance (Aug 11, 2024)
12-49336245-C-T		not specified	Uncertain significance (Oct 20, 2023)
12-49336267-G-T		not specified	Uncertain significance (Oct 24, 2024)
12-49336321-G-A		not specified	Uncertain significance (Dec 09, 2023)
12-49336330-G-A		not specified	Likely benign (Aug 05, 2024)
12-49336349-G-T		not specified	Uncertain significance (Dec 18, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C1QL4	protein_coding	protein_coding	ENST00000334221	2	4772

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.424	0.545	125566	0	9	125575	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.811	117	144	0.810	0.00000846	1486
Missense in Polyphen		44	56.344	0.78091		546
Synonymous	0.173	62	63.8	0.973	0.00000453	512
Loss of Function	1.73	1	5.29	0.189	2.27e-7	56

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000971	0.0000922
Ashkenazi Jewish	0.00	0.00
East Asian	0.000220	0.000218
Finnish	0.00	0.00
European (Non-Finnish)	0.0000189	0.0000176
Middle Eastern	0.000220	0.000218
South Asian	0.0000355	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May regulate the number of excitatory synapses that are formed on hippocampus neurons. Has no effect on inhibitory synapses (By similarity). May inhibit adipocyte differentiation at an early stage of the process (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.122

Haploinsufficiency Scores

• pHI: 0.266
• hipred: Y
• hipred_score: 0.634
• ghis: 0.404

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.508

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: C1ql4

Gene ontology

• Biological process: negative regulation of fat cell differentiation;negative regulation of fibroblast proliferation;negative regulation of ERK1 and ERK2 cascade
• Cellular component: collagen trimer;extracellular space
• Molecular function: identical protein binding