MEOX2

mesenchyme homeobox 2, the group of HOXL subclass homeoboxes

Basic information

Region (hg38): 7:15611211-15686683

Previous symbols: [ "GAX" ]

Links

ENSG00000106511 ∙ NCBI:4223 ∙ OMIM:600535 ∙ HGNC:7014 ∙ Uniprot:P50222 ∙ 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 MEOX2 gene.

• Inborn genetic diseases (9 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MEOX2 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			9			9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	0	0

Variants in MEOX2

This is a list of pathogenic ClinVar variants found in the MEOX2 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-15612458-G-C		not specified	Uncertain significance (Mar 11, 2022)
7-15612463-A-T		not specified	Uncertain significance (Jul 26, 2021)
7-15612489-C-G		not specified	Uncertain significance (Mar 16, 2023)
7-15685910-C-A		not specified	Uncertain significance (Apr 13, 2022)
7-15685951-C-A		not specified	Uncertain significance (Nov 21, 2023)
7-15685970-C-G		not specified	Uncertain significance (Jan 22, 2024)
7-15686048-C-T		not specified	Uncertain significance (Feb 05, 2024)
7-15686130-G-C		not specified	Uncertain significance (Jun 02, 2023)
7-15686131-T-C		not specified	Uncertain significance (Nov 23, 2021)
7-15686150-G-C		not specified	Uncertain significance (Jun 06, 2023)
7-15686167-T-G		not specified	Uncertain significance (Oct 18, 2021)
7-15686254-A-G		not specified	Uncertain significance (May 25, 2022)
7-15686360-T-C		not specified	Uncertain significance (Dec 09, 2023)
7-15686368-G-A		not specified	Uncertain significance (Dec 03, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MEOX2	protein_coding	protein_coding	ENST00000262041	3	75601

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.915	0.0849	124927	5	523	125455	0.00211

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.218	180	172	1.05	0.00000826	1983
Missense in Polyphen		55	73.996	0.74328		880
Synonymous	-1.72	90	71.5	1.26	0.00000368	588
Loss of Function	2.99	1	12.3	0.0812	6.10e-7	128

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00343	0.00229
Ashkenazi Jewish	0.000413	0.000199
East Asian	0.00	0.00
Finnish	0.00551	0.00241
European (Non-Finnish)	0.00780	0.00351
Middle Eastern	0.00	0.00
South Asian	0.00192	0.000916
Other	0.00382	0.00180

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Mesodermal transcription factor that plays a key role in somitogenesis and is required for sclerotome development (By similarity). Activates expression of CDKN1A and CDKN2A in endothelial cells, acting as a regulator of vascular cell proliferation. While it activates CDKN1A in a DNA-dependent manner, it activates CDKN2A in a DNA-independent manner (PubMed:22206000). May have a regulatory role when quiescent vascular smooth muscle cells reenter the cell cycle. {ECO:0000250|UniProtKB:P32443, ECO:0000269|PubMed:22206000}.
• Pathway: miR-targeted genes in lymphocytes - TarBase (Consensus)

Recessive Scores

• pRec: 0.146

Intolerance Scores

• loftool: 0.177
• rvis_EVS: -0.03
• rvis_percentile_EVS: 51.66

Haploinsufficiency Scores

• pHI: 0.855
• hipred: Y
• hipred_score: 0.737
• ghis: 0.529

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.741

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Meox2
• Phenotype: muscle phenotype; craniofacial phenotype; cellular phenotype; homeostasis/metabolism phenotype; 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); growth/size/body region phenotype; neoplasm; endocrine/exocrine gland phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue 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); limbs/digits/tail phenotype; digestive/alimentary phenotype; immune system phenotype; skeleton phenotype; renal/urinary system phenotype; embryo phenotype; respiratory system phenotype; liver/biliary system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); reproductive system 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); normal 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); hematopoietic system phenotype

Gene ontology

• Biological process: angiogenesis;somite specification;multicellular organism development;skeletal muscle tissue development;blood circulation;positive regulation of transcription by RNA polymerase II;roof of mouth development;limb development;somite development;negative regulation of cell migration involved in sprouting angiogenesis
• Cellular component: nucleus;cytoplasm;nuclear speck
• Molecular function: RNA polymerase II proximal promoter sequence-specific DNA binding;RNA polymerase II distal enhancer sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific;DNA-binding transcription factor activity;protein binding;sequence-specific DNA binding