MEOX2

protein-coding

mesenchyme homeobox 2, the group of HOXL subclass homeoboxes

Gene summary

This gene encodes a member of a subfamily of non-clustered, diverged, antennapedia-like homeobox-containing genes. The encoded protein may play a role in the regulation of vertebrate limb myogenesis. Mutations in the related mouse protein may be associated with craniofacial and/or skeletal abnormalities, in addition to neurovascular dysfunction observed in Alzheimer's disease. [provided by RefSeq, Jul 2008]

Previous symbols:

MANE transcript

NM_005924.5

Inheritance

—

ClinVar variants

U:48

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.08

Max pathogenic AF

—

Genomic locus

chr7:15,611,212-15,686,683

External References & Databases

Ensembl (ENSG00000106511)

Transcript & Mutation Effects

hg38 • Region Span ~75.5 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to MEOX2 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 48

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_005924.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			48 clinvar			48
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	48	0	0	48

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 5 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_005924.5	RefSeq	NP_005915.2	3	MANE Select
ENST00000262041.6	Ensembl	ENSP00000262041.5	3	MANE Select
ENST00000904167.1	Ensembl	ENSP00000574226.1	4	Standard
ENST00001012692.1	Ensembl	ENSP00000682509.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

miR-targeted genes in lymphocytes - TarBase

Biological Process

angiogenesis
somite specification
multicellular organism development
skeletal muscle tissue development
blood circulation

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

Cellular Component

nucleus
cytoplasm
nuclear speck

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000262041
Coding exons: 3
Length: 75601
Individuals with no LoFs: 124927
Homozygous LoFs: 5
Heterozygous LoFs: 523
Defined: 125455
p: 0.00211

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.218	180	172	1.05	0.00000826	1983
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0020	0.00087	notable
Latino/Admixed American	0.0014	0.00067	notable
Ashkenazi Jewish	0.00041	0.00020	rare
East Asian	0	0.0	absent
Finnish	0.0055	0.0024	notable
European (Non-Finnish)	0.0078	0.0035	notable
South Asian	0.0019	0.00092	notable
Other	0.0038	0.0018	notable

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.146

Intolerance Scores

LoFtool: 0.177
RVIS EVS: -0.03
RVIS percentile EVS: 51.66

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.741

Gene Damage Prediction

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