HMGXB4

HMG-box containing 4, the group of Non-canonical high mobility group

Basic information

Region (hg38): 22:35257452-35295807

Previous symbols: [ "HMG2L1" ]

Links

ENSG00000100281 ∙ NCBI:10042 ∙ OMIM:604702 ∙ HGNC:5003 ∙ Uniprot:Q9UGU5 ∙ 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 HMGXB4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HMGXB4 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			19		1	20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			2			2
Total	0	0	21	0	1

Variants in HMGXB4

This is a list of pathogenic ClinVar variants found in the HMGXB4 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-35262414-G-C		not specified	Uncertain significance (Jun 06, 2022)
22-35263203-A-G		not specified	Uncertain significance (Jul 14, 2023)
22-35263869-A-G		not specified	Uncertain significance (Aug 01, 2022)
22-35264654-C-T		not specified	Uncertain significance (Dec 22, 2023)
22-35264734-A-G		not specified	Uncertain significance (Aug 10, 2023)
22-35264882-G-T			Benign (Apr 19, 2019)
22-35264897-A-G		not specified	Uncertain significance (Feb 27, 2023)
22-35264915-A-G		not specified	Uncertain significance (Jul 26, 2024)
22-35264946-G-T		not specified	Uncertain significance (Dec 27, 2022)
22-35264986-G-A		not specified	Uncertain significance (Jul 31, 2024)
22-35265001-T-C		not specified	Uncertain significance (Jun 11, 2021)
22-35265041-C-T		not specified	Uncertain significance (Oct 08, 2024)
22-35265059-C-T		not specified	Uncertain significance (Oct 06, 2021)
22-35265094-C-T		not specified	Uncertain significance (Aug 17, 2022)
22-35265104-A-G		not specified	Uncertain significance (Oct 12, 2022)
22-35265134-G-A		not specified	Uncertain significance (Feb 06, 2023)
22-35265152-C-T		not specified	Uncertain significance (Jan 12, 2024)
22-35265172-C-G		not specified	Uncertain significance (Feb 27, 2024)
22-35265211-G-A		not specified	Uncertain significance (May 13, 2022)
22-35265334-A-C		not specified	Uncertain significance (Oct 13, 2023)
22-35265403-C-T		not specified	Uncertain significance (May 09, 2023)
22-35265434-C-G		not specified	Uncertain significance (Mar 21, 2024)
22-35265539-A-G		not specified	Uncertain significance (Jul 30, 2024)
22-35286029-G-T		not specified	Uncertain significance (Jan 24, 2024)
22-35287417-A-G		not specified	Uncertain significance (Nov 13, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HMGXB4	protein_coding	protein_coding	ENST00000216106	10	38356

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.494	0.506	125726	0	21	125747	0.0000835

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.24	251	313	0.803	0.0000159	3886
Missense in Polyphen		70	118.06	0.5929		1436
Synonymous	1.02	109	123	0.883	0.00000654	1177
Loss of Function	3.85	6	27.9	0.215	0.00000153	380

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000908	0.0000905
Ashkenazi Jewish	0.000241	0.000198
East Asian	0.0000603	0.0000544
Finnish	0.0000984	0.0000924
European (Non-Finnish)	0.000120	0.000114
Middle Eastern	0.0000603	0.0000544
South Asian	0.0000373	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Negatively regulates Wnt/beta-catenin signaling during development. {ECO:0000250}.

Recessive Scores

• pRec: 0.110

Intolerance Scores

• loftool: 0.550
• rvis_EVS: -0.49
• rvis_percentile_EVS: 22.36

Haploinsufficiency Scores

• pHI: 0.885
• hipred: Y
• hipred_score: 0.544
• ghis: 0.654

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.893

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hmgxb4

Gene ontology

• Biological process: endosome to lysosome transport;Wnt signaling pathway;negative regulation of Wnt signaling pathway
• Cellular component: NURF complex
• Molecular function: DNA binding