MNX1

motor neuron and pancreas homeobox 1, the group of HOXL subclass homeoboxes

Basic information

Region (hg38): 7:156994051-157010663

Previous symbols: [ "HLXB9" ]

Links

ENSG00000130675 ∙ NCBI:3110 ∙ OMIM:142994 ∙ HGNC:4979 ∙ Uniprot:P50219 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Currarino triad (Definitive), mode of inheritance: AD
• neonatal diabetes mellitus (Strong), mode of inheritance: AR
• permanent neonatal diabetes mellitus (Strong), mode of inheritance: AR
• Currarino triad (Strong), mode of inheritance: AR
• Currarino triad (Supportive), mode of inheritance: AD
• Currarino triad (Strong), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Currarino syndrome	AD	Oncologic	While congenital malformations often allow clinical recognition, individuals can have presacral teratomas, which can undergo malignant transformation, and awareness may allow prompt detection and management	Gastrointestinal; Genitourinary; Musculoskeletal; Oncologic; Renal	6789651; 2059799; 9843207; 10749657; 11528505; 15216552; 16906559; 17612791

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MNX1 gene.

• not provided (18 variants)
• Currarino triad (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MNX1 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			1	62	3	66
missense	1	3	124	6	1	135
nonsense	2		2			4
start loss	1					1
frameshift	16	3	2			21
inframe indel			25	8	7	40
splice donor/acceptor (+/-2bp)	1	2				3
splice region			2	2		4
non coding				12	10	22
Total	21	8	154	88	21

Variants in MNX1

This is a list of pathogenic ClinVar variants found in the MNX1 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-157005198-G-T			Likely benign (Jul 09, 2018)
7-157005288-C-T			Benign (Jul 09, 2018)
7-157005354-A-AG			Benign (Jul 09, 2018)
7-157005513-G-C		MNX1-related disorder	Likely benign (Sep 11, 2019)
7-157005528-G-GCGCGGGCTGGTGGCTGGGC		MNX1-related disorder	Likely pathogenic (Sep 06, 2022)
7-157005532-G-C			Likely benign (Aug 23, 2022)
7-157005533-G-A		Currarino triad	Likely benign (Jan 04, 2024)
7-157005534-G-A			Uncertain significance (Jul 10, 2023)
7-157005552-G-A			Uncertain significance (Oct 09, 2023)
7-157005555-G-A			Likely benign (Mar 26, 2023)
7-157005555-G-T			Uncertain significance (Dec 07, 2023)
7-157005558-G-C			Uncertain significance (Sep 15, 2022)
7-157005560-G-A			Uncertain significance (Oct 09, 2022)
7-157005564-C-A			Uncertain significance (Sep 09, 2022)
7-157005567-C-T			Uncertain significance (Sep 29, 2022)
7-157005570-C-T			Uncertain significance (May 31, 2022)
7-157005588-A-C			Uncertain significance (Aug 24, 2023)
7-157005589-G-C			Benign (Jan 03, 2024)
7-157005590-G-A		Currarino triad	Uncertain significance (Jan 04, 2022)
7-157005591-C-T			Uncertain significance (Feb 16, 2022)
7-157005592-G-A			Likely benign (Oct 17, 2022)
7-157005594-C-T		Inborn genetic diseases	Uncertain significance (May 06, 2022)
7-157005607-G-A			Likely benign (Aug 05, 2023)
7-157005622-G-A			Likely benign (Apr 30, 2023)
7-157005627-G-A			Uncertain significance (Apr 09, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MNX1	protein_coding	protein_coding	ENST00000252971	3	16601

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.788	0.211	120256	0	3	120259	0.0000125

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.731	133	159	0.837	0.00000724	2494
Missense in Polyphen		25	51.419	0.4862		558
Synonymous	0.489	71	76.4	0.929	0.00000368	880
Loss of Function	2.55	1	9.49	0.105	4.13e-7	114

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	0.0000487	0.0000480
European (Non-Finnish)	0.00000947	0.00000940
Middle Eastern	0.00	0.00
South Asian	0.0000328	0.0000328
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Putative transcription factor involved in pancreas development and function.
• Pathway: Maturity onset diabetes of the young - Homo sapiens (human) (Consensus)

Haploinsufficiency Scores

• pHI: 0.362

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.549

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mnx1
• Phenotype: digestive/alimentary 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); skeleton phenotype; immune system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system phenotype; growth/size/body region 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); normal 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); muscle phenotype; homeostasis/metabolism phenotype; cellular phenotype; endocrine/exocrine gland phenotype

Zebrafish Information Network

• Gene name: mnx1
• Affected structure: pancreatic B cell
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;humoral immune response;anatomical structure morphogenesis;spinal cord motor neuron cell fate specification;endocrine pancreas development;neuron projection morphogenesis
• Cellular component: nucleus;nucleolus;cytosol
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription factor activity;sequence-specific DNA binding