C1QL2

protein-coding

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

Gene summary

Predicted to enable identical protein binding activity. Predicted to be involved in maintenance of synapse structure and trans-synaptic signaling, modulating synaptic transmission. Predicted to be located in extracellular region. Predicted to be part of protein-containing complex. Predicted to be active in obsolete extracellular space; synapse; and synaptic cleft. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_182528.4

Inheritance

—

ClinVar variants

U:37B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.47

Max pathogenic AF

—

Genomic locus

chr2:119,156,243-119,158,751

External References & Databases

Ensembl (ENSG00000144119)

Transcript & Mutation Effects

hg38 • Region Span ~2.5 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to C1QL2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 36

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_182528.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar		1 clinvar	2
missense			36 clinvar			36
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	37	0	1	38

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 6 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_182528.4	RefSeq	NP_872334.2	2	MANE Select
ENST00000272520.4	Ensembl	ENSP00000272520.3	2	MANE Select
ENST00000850649.1	Ensembl	ENSP00000520925.1	2	Standard
ENST00000850649.2	Ensembl	ENSP00000521044.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

protein complex oligomerization

Molecular Function

identical protein binding

Cellular Component

extracellular region
collagen trimer

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000272520
Coding exons: 2
Length: 2647
Individuals with no LoFs: 125644
Homozygous LoFs: 0
Heterozygous LoFs: 5
Defined: 125649
p: 0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.65	96	154	0.625	0.00000686	1785
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000032	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0.000093	0.000092	rare
European (Non-Finnish)	0	0.0	absent
South Asian	0.000065	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.216

Gene Damage Prediction

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