HMGXB3

HMG-box containing 3, the group of Non-canonical high mobility group

Basic information

Region (hg38): 5:150000045-150053142

Previous symbols: [ "HMGX3" ]

Links

ENSG00000113716 ∙ NCBI:22993 ∙ OMIM:619800 ∙ HGNC:28982 ∙ Uniprot:Q12766 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Tourette syndrome (Limited), mode of inheritance: Unknown

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the HMGXB3 gene.

• Inborn genetic diseases (46 variants)
• not provided (7 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HMGXB3 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				2	1	3
missense			44	2	3	49
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region						0
non coding						0
Total	0	0	45	4	4

Variants in HMGXB3

This is a list of pathogenic ClinVar variants found in the HMGXB3 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-150004857-A-G		not specified	Uncertain significance (Dec 09, 2023)
5-150004991-T-C			Uncertain significance (Jan 11, 2022)
5-150006562-T-C		not specified	Uncertain significance (Aug 22, 2022)
5-150006635-A-T		not specified	Uncertain significance (Jul 21, 2022)
5-150006645-C-T		not specified	Uncertain significance (Jan 31, 2023)
5-150010208-G-C		not specified	Uncertain significance (May 16, 2023)
5-150010222-C-T		not specified	Uncertain significance (Jan 04, 2022)
5-150010223-G-A		not specified	Uncertain significance (Feb 28, 2023)
5-150010226-G-T		not specified	Uncertain significance (Feb 06, 2024)
5-150010268-C-A		not specified	Uncertain significance (Jun 06, 2023)
5-150010303-C-T		not specified	Uncertain significance (Aug 12, 2021)
5-150010330-A-T		not specified	Uncertain significance (Sep 16, 2021)
5-150010333-G-A		not specified	Uncertain significance (May 05, 2022)
5-150010349-C-T		not specified	Uncertain significance (Apr 25, 2023)
5-150010405-G-A			Benign (Apr 26, 2018)
5-150010453-G-A		not specified	Uncertain significance (Dec 08, 2023)
5-150010516-T-G		not specified	Uncertain significance (Apr 03, 2023)
5-150010597-A-G		not specified	Uncertain significance (Feb 16, 2023)
5-150012282-C-T			Benign (Dec 27, 2017)
5-150012297-A-G		not specified	Uncertain significance (Oct 30, 2023)
5-150012300-A-C		not specified	Uncertain significance (Sep 22, 2023)
5-150018606-G-T		not specified	Uncertain significance (Feb 17, 2022)
5-150018629-G-A		not specified	Uncertain significance (May 15, 2023)
5-150024401-C-T		not specified	Uncertain significance (Sep 26, 2023)
5-150024409-G-C		not specified	Uncertain significance (Feb 27, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HMGXB3	protein_coding	protein_coding	ENST00000502717	19	52503

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.000996	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.51	429	688	0.624	0.0000373	8331
Missense in Polyphen		126	268.58	0.46913		3360
Synonymous	3.15	211	278	0.760	0.0000155	2670
Loss of Function	5.70	7	50.9	0.138	0.00000253	649

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)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0844

Intolerance Scores

• rvis_EVS: 1.67
• rvis_percentile_EVS: 96.29

Haploinsufficiency Scores

• ghis: 0.383

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• gene_indispensability_pred: N
• gene_indispensability_score: 0.285

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hmgxb3
• Phenotype: homeostasis/metabolism phenotype; muscle phenotype; craniofacial phenotype; immune system phenotype; skeleton 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); hearing/vestibular/ear phenotype; vision/eye phenotype; 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); normal phenotype

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;biological_process;phosphorylation
• Cellular component: cellular_component;nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;kinase activity