C1QL1

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

Basic information

Region (hg38): 17:44959693-44968303

Links

ENSG00000131094 ∙ NCBI:10882 ∙ OMIM:611586 ∙ HGNC:24182 ∙ Uniprot:O75973 ∙ 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 C1QL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C1QL1 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			14			14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	0	0

Variants in C1QL1

This is a list of pathogenic ClinVar variants found in the C1QL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-44960201-A-G		not specified	Uncertain significance (May 23, 2023)
17-44960289-C-G		not specified	Uncertain significance (Dec 19, 2023)
17-44960310-T-C		not specified	Uncertain significance (Jul 25, 2023)
17-44967634-G-T		EBV-positive nodal T- and NK-cell lymphoma	Likely benign (-)
17-44967669-A-C		not specified	Uncertain significance (Aug 13, 2021)
17-44967700-C-A		not specified	Uncertain significance (Jun 17, 2024)
17-44967705-C-T		not specified	Uncertain significance (Apr 25, 2023)
17-44967711-G-A		not specified	Uncertain significance (May 31, 2023)
17-44967723-C-T		not specified	Uncertain significance (Oct 05, 2023)
17-44967733-C-G		not specified	Uncertain significance (Sep 25, 2023)
17-44967793-C-A		not specified	Uncertain significance (Jul 06, 2021)
17-44967823-C-T		not specified	Uncertain significance (Aug 15, 2023)
17-44967853-G-C		not specified	Uncertain significance (Mar 20, 2023)
17-44967870-G-C		not specified	Uncertain significance (Sep 20, 2023)
17-44967912-G-A		not specified	Uncertain significance (May 26, 2024)
17-44967925-C-T		not specified	Uncertain significance (Feb 13, 2023)
17-44967996-G-A		not specified	Uncertain significance (Oct 05, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C1QL1	protein_coding	protein_coding	ENST00000253407	2	8379

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000562	0.147	125697	0	18	125715	0.0000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.25	96	137	0.699	0.00000684	1655
Missense in Polyphen		34	58.006	0.58615		626
Synonymous	1.34	50	63.6	0.787	0.00000368	553
Loss of Function	-0.719	7	5.23	1.34	2.23e-7	64

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000377	0.000377
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000266	0.0000264
Middle Eastern	0.000109	0.000109
South Asian	0.00	0.00
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). {ECO:0000250}.

Recessive Scores

• pRec: 0.122

Haploinsufficiency Scores

• pHI: 0.214
• ghis: 0.604

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.336

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: C1ql1
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Gene ontology

• Biological process: locomotory behavior;neuron remodeling;motor learning;maintenance of synapse structure
• Cellular component: cellular_component;collagen trimer;cytoplasm;synaptic cleft;climbing fiber;presynapse
• Molecular function: molecular_function;signaling receptor binding;protein binding