BARHL1

BarH like homeobox 1, the group of NKL subclass homeoboxes and pseudogenes

Basic information

Region (hg38): 9:132582606-132590252

Links

ENSG00000125492 ∙ NCBI:56751 ∙ OMIM:605211 ∙ HGNC:953 ∙ Uniprot:Q9BZE3 ∙ 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 BARHL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BARHL1 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			22			22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	0	0

Variants in BARHL1

This is a list of pathogenic ClinVar variants found in the BARHL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-132582846-G-A		not specified	Uncertain significance (Nov 09, 2022)
9-132582864-C-T		not specified	Uncertain significance (Oct 30, 2024)
9-132582940-G-A		not specified	Uncertain significance (Dec 02, 2024)
9-132582951-G-A		not specified	Uncertain significance (Jul 25, 2024)
9-132582958-C-G		not specified	Uncertain significance (Jul 07, 2022)
9-132582991-G-A		not specified	Uncertain significance (Nov 08, 2024)
9-132583000-G-A		not specified	Uncertain significance (Apr 29, 2024)
9-132583021-A-G		not specified	Uncertain significance (Jan 16, 2024)
9-132583116-C-T		not specified	Uncertain significance (Sep 12, 2023)
9-132583132-C-A		not specified	Uncertain significance (Oct 03, 2022)
9-132583150-G-C		not specified	Uncertain significance (Jun 11, 2021)
9-132583183-T-A		not specified	Uncertain significance (Jan 04, 2022)
9-132583186-C-T		not specified	Uncertain significance (Nov 10, 2024)
9-132587362-C-T		not specified	Uncertain significance (Sep 30, 2021)
9-132587383-G-T		not specified	Uncertain significance (Jun 18, 2021)
9-132587475-G-A		not specified	Uncertain significance (Mar 07, 2025)
9-132587517-G-A		not specified	Uncertain significance (Jun 21, 2022)
9-132589274-G-A		not specified	Uncertain significance (Jun 03, 2024)
9-132589311-C-G		not specified	Uncertain significance (Jan 03, 2025)
9-132589358-G-C		not specified	Uncertain significance (Aug 21, 2024)
9-132589365-C-T		not specified	Uncertain significance (Mar 11, 2025)
9-132589379-C-T		not specified	Uncertain significance (May 17, 2023)
9-132589432-C-G		not specified	Uncertain significance (Jan 30, 2024)
9-132589467-C-T		not specified	Uncertain significance (Mar 09, 2025)
9-132589469-C-G		not specified	Uncertain significance (Feb 24, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BARHL1	protein_coding	protein_coding	ENST00000263610	3	8082

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.146	0.838	125693	0	7	125700	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.09	151	194	0.780	0.00000914	2066
Missense in Polyphen		42	61.902	0.67849		621
Synonymous	-0.265	96	92.8	1.03	0.00000467	731
Loss of Function	2.07	3	10.1	0.297	4.29e-7	118

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000640	0.0000615
Ashkenazi Jewish	0.0000995	0.0000993
East Asian	0.00	0.00
Finnish	0.0000929	0.0000924
European (Non-Finnish)	0.0000277	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.160

Intolerance Scores

• loftool: 0.166
• rvis_EVS: -0.36
• rvis_percentile_EVS: 28.63

Haploinsufficiency Scores

• pHI: 0.806
• hipred: N
• hipred_score: 0.459
• ghis: 0.542

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.946

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Barhl1
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); hearing/vestibular/ear 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)

Gene ontology

• Biological process: neuron migration;regulation of transcription by RNA polymerase II;nervous system development;sensory perception of sound;tissue development;midbrain development;negative regulation of neuron apoptotic process;positive regulation of transcription by RNA polymerase II;animal organ 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