BARX1

BARX homeobox 1, the group of NKL subclass homeoboxes and pseudogenes

Basic information

Region (hg38): 9:93951627-93955355

Links

ENSG00000131668

∙ NCBI:56033 ∙ OMIM:603260 ∙ HGNC:955 ∙ Uniprot:Q9HBU1 ∙ 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 BARX1 gene.

not_specified (33 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BARX1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000021570.4. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			33 clinvar			33
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	33	0	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BARX1	protein_coding	protein_coding	ENST00000253968	4	3750

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.586	0.405	125648	0	1	125649	0.00000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.07	75	106	0.708	0.00000472	1567
Missense in Polyphen		31	46.832	0.66194		625
Synonymous	0.166	49	50.5	0.970	0.00000231	540
Loss of Function	2.09	1	6.95	0.144	2.94e-7	104

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	0.00	0.00
European (Non-Finnish)	0.00000880	0.00000880
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Transcription factor, which is involved in craniofacial development, in odontogenesis and in stomach organogenesis. May have a role in the differentiation of molars from incisors. Plays a role in suppressing endodermal Wnt activity (By similarity). Binds to a regulatory module of the NCAM promoter. {ECO:0000250, ECO:0000269|PubMed:9804553}.;

Recessive Scores

pRec: 0.178

Haploinsufficiency Scores

pHI: 0.200
hipred: Y
hipred_score: 0.634
ghis: 0.408

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.875

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Barx1
Phenotype: cellular phenotype; craniofacial phenotype; growth/size/body region phenotype; digestive/alimentary 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);

Zebrafish Information Network

Gene name: barx1
Affected structure: chondroblast
Phenotype tag: abnormal
Phenotype quality: absent

Gene ontology

Biological process: regulation of transcription by RNA polymerase II;cell-cell signaling;tissue development;anterior/posterior pattern specification;negative regulation of Wnt signaling pathway;epithelial cell differentiation;positive regulation of transcription by RNA polymerase II;animal organ development;spleen development;digestive system development
Cellular component: nucleus
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 transcription factor activity