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): 15:73051709-73305205

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.

• Inborn genetic diseases (54 variants)
• not provided (6 variants)
• NEO1-related condition (2 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.

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					3	3
missense			55	3		58
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	55	3	3

Variants in NEO1

This is a list of pathogenic ClinVar variants found in the NEO1 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-73052719-C-A		not specified	Uncertain significance (May 08, 2023)
15-73052728-T-C			Uncertain significance (Aug 01, 2022)
15-73052778-A-T		not specified	Uncertain significance (Oct 03, 2022)
15-73116673-A-G		NEO1-related disorder	Likely benign (Nov 07, 2019)
15-73116684-T-C		not specified	Uncertain significance (May 10, 2022)
15-73116704-G-A		not specified	Uncertain significance (Jun 21, 2022)
15-73116768-A-G		not specified	Uncertain significance (Feb 27, 2024)
15-73122533-A-G		not specified	Uncertain significance (Aug 30, 2021)
15-73122547-A-G		NEO1-related disorder	Benign (Oct 21, 2019)
15-73122579-A-G		not specified	Likely benign (Dec 03, 2021)
15-73122618-C-T		NEO1-related disorder	Likely benign (Jun 12, 2022)
15-73122689-A-T		not specified	Uncertain significance (Mar 23, 2022)
15-73122739-C-T		NEO1-related disorder	Benign/Likely benign (May 01, 2019)
15-73122740-G-A		not specified	Likely benign (Dec 16, 2023)
15-73122782-G-A		not specified	Uncertain significance (Jun 21, 2021)
15-73126400-ATT-A		NEO1-related disorder	Benign (Jun 06, 2019)
15-73126411-T-G		NEO1-related disorder	Likely benign (Apr 03, 2019)
15-73126429-T-A		not specified	Uncertain significance (May 03, 2023)
15-73126439-G-C		not specified	Uncertain significance (Feb 21, 2024)
15-73126543-A-G		not specified	Uncertain significance (Nov 09, 2023)
15-73135863-CTTT-C		NEO1-related disorder	Benign (Feb 19, 2019)
15-73135863-CTTTT-C		NEO1-related disorder	Benign (Mar 25, 2019)
15-73135863-CTTTTT-C		NEO1-related disorder	Likely benign (Jan 06, 2020)
15-73135883-T-A		NEO1-related disorder	Benign (Dec 31, 2019)
15-73135919-G-A		not specified	Uncertain significance (Feb 02, 2022)

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