C1QL2

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

Basic information

Region (hg38): 2:119156243-119158751

Links

ENSG00000144119 ∙ NCBI:165257 ∙ OMIM:614330 ∙ HGNC:24181 ∙ Uniprot:Q7Z5L3 ∙ 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 C1QL2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C1QL2 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
missense			17			17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	0	1

Variants in C1QL2

This is a list of pathogenic ClinVar variants found in the C1QL2 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-119156810-G-A		not specified	Uncertain significance (Jan 16, 2025)
2-119156857-C-T		not specified	Uncertain significance (Feb 04, 2025)
2-119156911-T-G		not specified	Uncertain significance (Aug 15, 2023)
2-119157591-C-G		not specified	Uncertain significance (Dec 18, 2023)
2-119157702-G-T		not specified	Uncertain significance (Sep 01, 2021)
2-119157858-C-T		not specified	Uncertain significance (Jan 31, 2023)
2-119157887-C-T		not specified	Uncertain significance (Sep 17, 2021)
2-119157889-G-T		not specified	Uncertain significance (Feb 08, 2025)
2-119157894-C-T		not specified	Uncertain significance (Aug 26, 2022)
2-119157896-G-A		not specified	Uncertain significance (Dec 19, 2023)
2-119157926-C-T		not specified	Uncertain significance (Jan 16, 2025)
2-119157977-G-A		not specified	Uncertain significance (Dec 12, 2023)
2-119157993-G-C		not specified	Uncertain significance (Jul 15, 2024)
2-119158013-T-C		not specified	Uncertain significance (Aug 15, 2023)
2-119158019-G-A		not specified	Uncertain significance (May 03, 2023)
2-119158032-C-A		not specified	Uncertain significance (Sep 13, 2022)
2-119158040-G-A		not specified	Uncertain significance (Feb 19, 2025)
2-119158065-G-A		not specified	Uncertain significance (Aug 02, 2021)
2-119158072-G-T		not specified	Uncertain significance (May 24, 2023)
2-119158143-C-T		not specified	Uncertain significance (Jan 26, 2022)
2-119158170-C-A		not specified	Uncertain significance (Nov 18, 2022)
2-119158174-G-T			Benign (Dec 31, 2019)
2-119158224-C-T		not specified	Uncertain significance (Feb 25, 2025)
2-119158241-G-A		not specified	Uncertain significance (Jan 11, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C1QL2	protein_coding	protein_coding	ENST00000272520	2	2647

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0357	0.840	125644	0	5	125649	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.65	96	154	0.625	0.00000686	1785
Missense in Polyphen		23	51.354	0.44788		580
Synonymous	-0.720	75	67.5	1.11	0.00000322	592
Loss of Function	1.23	3	6.33	0.474	2.68e-7	79

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000319	0.0000319
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000929	0.0000924
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.0000653	0.0000653
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: 0.118

Haploinsufficiency Scores

• pHI: 0.144
• hipred: Y
• hipred_score: 0.670
• ghis: 0.441

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.216

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: C1ql2

Gene ontology

• Biological process: protein complex oligomerization
• Cellular component: extracellular region;collagen trimer
• Molecular function: identical protein binding