NEO1

neogenin 1, the group of Fibronectin type III domain containing|I-set domain containing|Ig-like cell adhesion molecule family

Basic information

Region (hg38): 15:73051710-73305205

Links

ENSG00000067141

∙ NCBI:4756 ∙ OMIM:601907 ∙ HGNC:7754 ∙ Uniprot:Q92859 ∙ 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 NEO1 gene.

not_specified (167 variants)
NEO1-related_disorder (26 variants)
not_provided (6 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NEO1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000002499.4. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				6 clinvar	5 clinvar	11
missense			170 clinvar	7 clinvar		177
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)					1 clinvar	1
Total	0	0	170	13	6

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NEO1	protein_coding	protein_coding	ENST00000339362	29	253497

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.244	0.756	125719	0	29	125748	0.000115

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.63	673	803	0.838	0.0000430	9480
Missense in Polyphen		263	379.01	0.69392		4330
Synonymous	0.847	275	293	0.937	0.0000162	2959
Loss of Function	6.11	17	73.5	0.231	0.00000438	817

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000462	0.000461
Ashkenazi Jewish	0.0000995	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.000231	0.000231
European (Non-Finnish)	0.000106	0.000105
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Multi-functional cell surface receptor regulating cell adhesion in many diverse developmental processes, including neural tube and mammary gland formation, myogenesis and angiogenesis. Receptor for members of the BMP, netrin, and repulsive guidance molecule (RGM) families. Netrin-Neogenin interactions result in a chemoattractive axon guidance response and cell-cell adhesion, the interaction between NEO1/Neogenin and RGMa and RGMb induces a chemorepulsive response. {ECO:0000269|PubMed:21149453}.;
Pathway: Cell adhesion molecules (CAMs) - Homo sapiens (human);Splicing factor NOVA regulated synaptic proteins;Developmental Biology;CDO in myogenesis;Myogenesis;Netrin-1 signaling;Axon guidance (Consensus)

Recessive Scores

pRec: 0.180

Intolerance Scores

loftool: 0.320
rvis_EVS: -1.3
rvis_percentile_EVS: 4.95

Haploinsufficiency Scores

pHI: 0.263
hipred: Y
hipred_score: 0.746
ghis: 0.549

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.645

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Neo1
Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); 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); integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); endocrine/exocrine gland phenotype;

Zebrafish Information Network

Gene name: neo1a
Affected structure: neuroepithelial cell
Phenotype tag: abnormal
Phenotype quality: decreased amount

Gene ontology

Biological process: cell adhesion;axon guidance;positive regulation of BMP signaling pathway;iron ion homeostasis
Cellular component: nucleoplasm;Golgi apparatus;plasma membrane;integral component of plasma membrane;plasma membrane protein complex
Molecular function: protein binding;signaling receptor activity;co-receptor binding