NRGN

neurogranin

Basic information

Region (hg38): 11:124739942-124747210

Links

ENSG00000154146

∙ NCBI:4900 ∙ OMIM:602350 ∙ HGNC:8000 ∙ Uniprot:Q92686 ∙ 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 NRGN gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NRGN 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			4 clinvar			4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	4	0	0

Variants in NRGN

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

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

Position	Phenotype	Significance	ClinVar
11-124745506-A-C	not specified	Uncertain significance (Jun 28, 2023)	2606878
11-124745608-A-G	not specified	Uncertain significance (Nov 09, 2023)	3202125
11-124745641-G-C	not specified	Uncertain significance (Jul 26, 2022)	2303574
11-124745666-G-A	not specified	Uncertain significance (May 05, 2022)	2287626

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NRGN	protein_coding	protein_coding	ENST00000284292	2	7365

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.482	0.443	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.70	15	48.2	0.311	0.00000315	487
Missense in Polyphen		0	1.0648	0		17
Synonymous	1.69	12	22.1	0.542	0.00000173	164
Loss of Function	1.23	0	1.78	0.00	7.95e-8	28

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Acts as a "third messenger" substrate of protein kinase C-mediated molecular cascades during synaptic development and remodeling. Binds to calmodulin in the absence of calcium (By similarity). {ECO:0000250}.;

Recessive Scores

pRec: 0.194

Haploinsufficiency Scores

pHI: 0.395
hipred: Y
hipred_score: 0.621
ghis: 0.667

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.114

Mouse Genome Informatics

Gene name: Nrgn
Phenotype: 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan);

Gene ontology

Biological process: signal transduction;nervous system development;associative learning;telencephalon development;postsynaptic modulation of chemical synaptic transmission;positive regulation of long-term synaptic potentiation
Cellular component: nucleus;cytoplasm;trans-Golgi network transport vesicle membrane;postsynaptic density;axon;mitochondrial membrane;neuronal cell body;dendritic spine head;postsynaptic membrane;glutamatergic synapse
Molecular function: calmodulin binding;phosphatidylinositol-3,4,5-trisphosphate binding;phosphatidic acid binding