HLX

H2.0 like homeobox, the group of NKL subclass homeoboxes and pseudogenes

Basic information

Region (hg38): 1:220879431-220885059

Previous symbols: [ "HLX1" ]

Links

ENSG00000136630 ∙ NCBI:3142 ∙ OMIM:142995 ∙ HGNC:4978 ∙ Uniprot:Q14774 ∙ 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 HLX gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HLX 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			22	1	1	24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	22	2	2

Variants in HLX

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

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

Position	Type	Phenotype	Significance	ClinVar
1-220879885-T-A		not specified	Uncertain significance (Dec 08, 2023)
1-220879915-G-T		not specified	Uncertain significance (Feb 15, 2023)
1-220879953-C-G		not specified	Uncertain significance (Sep 27, 2024)
1-220879990-T-A		not specified	Uncertain significance (Aug 02, 2021)
1-220880002-A-G		not specified	Uncertain significance (Apr 24, 2024)
1-220880008-C-T		not specified	Uncertain significance (Sep 16, 2021)
1-220880018-T-G		not specified	Uncertain significance (Jun 11, 2021)
1-220880149-G-C		not specified	Uncertain significance (Mar 31, 2022)
1-220880157-G-A		HLX-related disorder	Likely benign (Mar 11, 2024)
1-220880159-C-T		not specified	Uncertain significance (May 23, 2023)
1-220880161-T-A		not specified	Uncertain significance (Aug 20, 2024)
1-220880189-G-A		not specified	Uncertain significance (Jan 26, 2023)
1-220880335-C-A		not specified	Uncertain significance (Mar 19, 2024)
1-220880339-A-C		not specified	Uncertain significance (Sep 15, 2021)
1-220880356-C-T		HLX-related disorder	Likely benign (Feb 22, 2022)
1-220880359-G-C		not specified	Uncertain significance (Jul 13, 2022)
1-220880391-T-C		HLX-related disorder	Likely benign (Dec 07, 2022)
1-220880393-A-G		not specified	Uncertain significance (Sep 30, 2024)
1-220881229-G-A		not specified	Uncertain significance (May 26, 2022)
1-220881260-C-T		not specified	Uncertain significance (Jan 03, 2022)
1-220881289-A-G		not specified	Uncertain significance (Jul 28, 2021)
1-220881298-G-T		not specified	Uncertain significance (Aug 28, 2024)
1-220881299-C-T		not specified	Uncertain significance (Aug 28, 2024)
1-220881305-C-T			Benign (Dec 31, 2019)
1-220882215-A-G		not specified	Uncertain significance (Mar 30, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HLX	protein_coding	protein_coding	ENST00000366903	4	6703

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.883	0.117	125743	0	5	125748	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.377	275	293	0.938	0.0000155	3110
Missense in Polyphen		73	86.88	0.84024		932
Synonymous	-0.619	148	139	1.07	0.00000850	1052
Loss of Function	3.21	2	15.8	0.127	7.32e-7	157

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000621	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000554	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000177	0.0000176
Middle Eastern	0.0000554	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcription factor required for TBX21/T-bet-dependent maturation of Th1 cells as well as maintenance of Th1-specific gene expression. Involved in embryogenesis and hematopoiesis (By similarity). {ECO:0000250}.
• Pathway: TYROBP Causal Network;IL12-mediated signaling events (Consensus)

Recessive Scores

• pRec: 0.157

Intolerance Scores

• loftool: 0.222
• rvis_EVS: 0.62
• rvis_percentile_EVS: 83.36

Haploinsufficiency Scores

• pHI: 0.242
• hipred: Y
• hipred_score: 0.715
• ghis: 0.467

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.412

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hlx
• 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); digestive/alimentary phenotype; liver/biliary system phenotype; respiratory 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); hematopoietic system phenotype; endocrine/exocrine gland phenotype; muscle 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

Zebrafish Information Network

• Gene name: hlx1
• Affected structure: intersegmental vein
• Phenotype tag: abnormal
• Phenotype quality: shortened

Gene ontology

• Biological process: liver development;regulation of transcription by RNA polymerase II;multicellular organism development;skeletal muscle tissue development;positive regulation of cell population proliferation;cell differentiation;positive regulation of T-helper 1 cell differentiation;negative regulation of T-helper 2 cell differentiation;positive regulation of organ growth;enteric nervous system development;embryonic digestive tract morphogenesis
• Cellular component: nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;protein binding;sequence-specific DNA binding