NEGR1

neuronal growth regulator 1, the group of I-set domain containing|IgLON cell adhesion molecules

Basic information

Region (hg38): 1:71395942-72282539

Links

ENSG00000172260 ∙ NCBI:257194 ∙ OMIM:613173 ∙ HGNC:17302 ∙ Uniprot:Q7Z3B1 ∙ 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 NEGR1 gene.

• not provided (6 variants)
• Inborn genetic diseases (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NEGR1 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				2	2	4
missense			5	1	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	5	3	3

Variants in NEGR1

This is a list of pathogenic ClinVar variants found in the NEGR1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-71407462-T-G		not specified	Uncertain significance (Jun 29, 2023)
1-71407536-G-A			Benign (Dec 31, 2019)
1-71592927-C-T		NEGR1-related disorder	Likely benign (Jun 06, 2023)
1-71611074-C-G		not specified	Uncertain significance (Aug 01, 2022)
1-71611107-G-A		not specified	Uncertain significance (Dec 11, 2023)
1-71611112-G-T			Benign (Dec 31, 2019)
1-71611116-C-A		not specified	Uncertain significance (Mar 31, 2022)
1-71698078-C-T			Likely benign (Jan 01, 2023)
1-71776201-G-C		not specified	Uncertain significance (Oct 29, 2021)
1-71935195-T-C		not specified	Uncertain significance (Sep 29, 2023)
1-71935256-T-G		not specified	Uncertain significance (Feb 13, 2024)
1-72282328-G-A		not specified	Uncertain significance (Jul 08, 2022)
1-72282401-G-C			Benign (Dec 31, 2019)
1-72282435-C-A			Likely benign (Jul 31, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NEGR1	protein_coding	protein_coding	ENST00000357731	7	886795

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.992	0.00827	125744	0	3	125747	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.64	135	200	0.674	0.0000103	2299
Missense in Polyphen		30	69.375	0.43243		762
Synonymous	-0.344	82	78.1	1.05	0.00000435	705
Loss of Function	3.80	1	18.8	0.0533	0.00000104	202

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)	0.00000889	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.000167	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in cell-adhesion. May function as a trans-neural growth-promoting factor in regenerative axon sprouting in the mammalian brain (By similarity). {ECO:0000250}.
• Pathway: Cell adhesion molecules (CAMs) - Homo sapiens (human);Post-translational modification: synthesis of GPI-anchored proteins;Post-translational protein modification;Metabolism of proteins (Consensus)

Recessive Scores

• pRec: 0.136

Intolerance Scores

• loftool: 0.316
• rvis_EVS: -0.27
• rvis_percentile_EVS: 34.6

Haploinsufficiency Scores

• pHI: 0.127
• hipred: Y
• hipred_score: 0.707
• ghis: 0.540

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.462

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Negr1
• Phenotype: hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system 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); liver/biliary system phenotype; immune system phenotype; growth/size/body region phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: locomotory behavior;feeding behavior;positive regulation of neuron projection development;cell-cell adhesion
• Cellular component: extracellular region;plasma membrane;anchored component of membrane
• Molecular function: protein binding