NRN1

neuritin 1

Basic information

Region (hg38): 6:5997999-6007605

Links

ENSG00000124785 ∙ NCBI:51299 ∙ OMIM:607409 ∙ HGNC:17972 ∙ Uniprot:Q9NPD7 ∙ 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 NRN1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NRN1 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	2	1	7
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	2	1

Variants in NRN1

This is a list of pathogenic ClinVar variants found in the NRN1 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-5998981-A-G		not specified	Uncertain significance (Sep 09, 2024)
6-5999008-A-G		not specified	Uncertain significance (Jan 26, 2022)
6-5999014-A-C		not specified	Uncertain significance (Apr 07, 2023)
6-5999030-G-C		not specified	Likely benign (May 05, 2022)
6-5999032-A-G		not specified	Likely benign (Apr 07, 2023)
6-5999071-C-T		not specified	Uncertain significance (May 27, 2022)
6-6002459-C-T		not specified	Uncertain significance (Aug 23, 2021)
6-6006731-C-T			Benign (Dec 04, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NRN1	protein_coding	protein_coding	ENST00000244766	3	8969

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.860	0.138	125064	0	1	125065	0.00000400

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.14	53	82.2	0.645	0.00000367	921
Missense in Polyphen		8	23.694	0.33764		282
Synonymous	-0.467	42	38.3	1.10	0.00000177	283
Loss of Function	2.35	0	6.45	0.00	3.45e-7	71

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)	0.00000885	0.00000885
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Promotes neurite outgrowth and especially branching of neuritic processes in primary hippocampal and cortical cells. {ECO:0000250}.
• Pathway: Post-translational modification: synthesis of GPI-anchored proteins;Post-translational protein modification;Metabolism of proteins (Consensus)

Recessive Scores

• pRec: 0.155

Intolerance Scores

• loftool: 0.101
• rvis_EVS: 0.15
• rvis_percentile_EVS: 64.11

Haploinsufficiency Scores

• pHI: 0.515
• hipred: Y
• hipred_score: 0.735
• ghis: 0.520

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.283

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nrn1
• 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); cellular phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: nervous system development
• Cellular component: extracellular region;plasma membrane;cell junction;anchored component of membrane;synapse