BARX2

BARX homeobox 2, the group of NKL subclass homeoboxes and pseudogenes

Basic information

Region (hg38): 11:129375848-129452279

Links

ENSG00000043039 ∙ NCBI:8538 ∙ OMIM:604823 ∙ HGNC:956 ∙ Uniprot:Q9UMQ3 ∙ 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 BARX2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BARX2 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	1
missense			25	1	1	27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	25	1	2

Variants in BARX2

This is a list of pathogenic ClinVar variants found in the BARX2 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-129376043-G-A		not specified	Uncertain significance (Jul 14, 2021)
11-129376058-G-C		not specified	Uncertain significance (Aug 20, 2024)
11-129376090-A-G		not specified	Uncertain significance (Dec 26, 2023)
11-129376102-A-G		not specified	Uncertain significance (Jan 22, 2024)
11-129376139-C-A		not specified	Uncertain significance (Oct 01, 2024)
11-129436766-G-A		not specified	Uncertain significance (Dec 02, 2024)
11-129436813-T-C		not specified	Uncertain significance (Oct 10, 2023)
11-129436816-C-T		not specified	Uncertain significance (Feb 12, 2024)
11-129436825-C-G		not specified	Uncertain significance (Mar 03, 2022)
11-129436835-C-T		not specified	Uncertain significance (Jun 10, 2024)
11-129436853-T-G		not specified	Uncertain significance (May 26, 2024)
11-129436910-T-C		not specified	Uncertain significance (Jan 04, 2024)
11-129436919-G-C		not specified	Uncertain significance (Jun 11, 2021)
11-129436949-G-A		not specified	Uncertain significance (Sep 05, 2024)
11-129436956-G-T		not specified	Uncertain significance (Feb 22, 2025)
11-129436966-C-T		not specified	Uncertain significance (Nov 15, 2023)
11-129436978-A-G		not specified	Uncertain significance (Nov 13, 2024)
11-129436987-G-A		not specified	Uncertain significance (Jan 31, 2025)
11-129436990-C-A		not specified	Uncertain significance (Aug 20, 2024)
11-129437028-G-A			Benign (Apr 19, 2018)
11-129437041-A-T		not specified	Uncertain significance (Apr 21, 2022)
11-129437045-C-T		not specified	Uncertain significance (Feb 12, 2025)
11-129442897-G-A		not specified	Uncertain significance (Jun 07, 2024)
11-129451170-C-T		not specified	Uncertain significance (May 31, 2023)
11-129451235-A-C		not specified	Uncertain significance (Aug 12, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BARX2	protein_coding	protein_coding	ENST00000281437	4	76337

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.212	0.780	125739	0	7	125746	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0895	171	168	1.02	0.00000948	1781
Missense in Polyphen		64	66.622	0.96065		738
Synonymous	0.410	68	72.4	0.939	0.00000432	570
Loss of Function	2.29	3	11.3	0.266	5.61e-7	127

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	0.0000462	0.0000462
European (Non-Finnish)	0.0000357	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.0000656	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcription factor. Binds optimally to the DNA consensus sequence 5'-YYTAATGRTTTTY-3'. May control the expression of neural adhesion molecules such as L1 or Ng-CAM during embryonic development of both the central and peripherical nervous system. May be involved in controlling adhesive processes in keratinizing epithelia (By similarity). {ECO:0000250}.
• Pathway: Preimplantation Embryo (Consensus)

Recessive Scores

• pRec: 0.109

Intolerance Scores

• loftool: 0.352
• rvis_EVS: -0.18
• rvis_percentile_EVS: 40.16

Haploinsufficiency Scores

• pHI: 0.240
• hipred: Y
• hipred_score: 0.690
• ghis: 0.481

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.245

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Barx2
• Phenotype: homeostasis/metabolism phenotype; muscle phenotype; endocrine/exocrine gland 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; skeleton phenotype; vision/eye phenotype; limbs/digits/tail phenotype; pigmentation 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); 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;cartilage condensation;regulation of transcription by RNA polymerase II;tissue development;myotube differentiation;positive regulation of transcription by RNA polymerase II;animal organ development
• Cellular component: nucleus;nucleoplasm;transcription factor complex;cytosol
• Molecular function: RNA polymerase II regulatory region sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific;DNA binding;chromatin binding