CNPY4

protein-coding

canopy FGF signaling regulator 4

Gene summary

Predicted to enable signaling receptor binding activity. Involved in positive regulation of protein localization to plasma membrane. Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_152755.2

Inheritance

—

ClinVar variants

U:43B:3

Top phenotype

Autism

gnomAD constraint

pLI —, LoF o/e 1.22

Max pathogenic AF

—

Genomic locus

chr7:100,119,634-100,125,508

External References & Databases

Ensembl (ENSG00000166997)

Transcript & Mutation Effects

hg38 • Region Span ~5.9 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 CNPY4 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 38

not providedTotal: 1

AutismTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_152755.2. 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			2 clinvar	1 clinvar		3
missense			37 clinvar	2 clinvar		39
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	43	3	0	46

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 20 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_152755.2	RefSeq	NP_689968.1	6	MANE Select
ENST00000262932.5	Ensembl	ENSP00000262932.3	6	MANE Select
ENST00000462193.2	Ensembl	ENSP00000488873.1	4	Standard
ENST00000483756.5	Ensembl	ENSP00000488362.1	1	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

positive regulation of protein localization to plasma membrane

Molecular Function

molecular_function
signaling receptor binding

Cellular Component

extracellular region

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000262932
Coding exons: 6
Length: 5899
Individuals with no LoFs: 125644
Homozygous LoFs: 0
Heterozygous LoFs: 104
Defined: 125748
p: 0.000414

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.255	147	139	1.06	0.00000715	1612
Missense (PolyPhen)		54	57.373	0.94121		673
Synonymous	0.145	52	53.4	0.975	0.00000287	463
Loss of Function	-0.795	18	14.7	1.22	8.57e-7	153

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00062	0.00062	rare
Latino/Admixed American	0.00041	0.00040	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.0012	0.0012	notable
Finnish	0.000093	0.000092	rare
European (Non-Finnish)	0.00040	0.00040	rare
South Asian	0.00029	0.00029	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Plays a role in the regulation of the cell surface expression of TLR4. {ECO:0000269|PubMed:16338228}.;

Recessive Scores

pRec: 0.106

Intolerance Scores

LoFtool: 0.825
RVIS EVS: 0.26
RVIS percentile EVS: 70.26

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.327

Gene Damage Prediction

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