HMGB4

high mobility group box 4, the group of Canonical high mobility group

Basic information

Region (hg38): 1:33860475-33864791

Links

ENSG00000176256 ∙ NCBI:127540 ∙ OMIM:617285 ∙ HGNC:24954 ∙ Uniprot:Q8WW32 ∙ 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 HMGB4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HMGB4 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			14			14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	0	0

Variants in HMGB4

This is a list of pathogenic ClinVar variants found in the HMGB4 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-33864232-C-G		not specified	Uncertain significance (Nov 07, 2024)
1-33864253-T-G		not specified	Uncertain significance (Jun 26, 2024)
1-33864285-C-T		not specified	Uncertain significance (Sep 26, 2024)
1-33864316-C-T		not specified	Uncertain significance (Jan 18, 2022)
1-33864331-A-T		not specified	Uncertain significance (Jun 24, 2022)
1-33864370-A-G		not specified	Uncertain significance (Jan 19, 2024)
1-33864379-T-C		not specified	Uncertain significance (Jun 24, 2022)
1-33864381-G-A		not specified	Uncertain significance (Feb 05, 2025)
1-33864400-G-A		not specified	Uncertain significance (Nov 09, 2024)
1-33864475-G-A		not specified	Uncertain significance (Feb 20, 2025)
1-33864511-A-G		not specified	Uncertain significance (Jan 18, 2025)
1-33864538-C-T		not specified	Uncertain significance (Dec 20, 2023)
1-33864545-G-T		not specified	Uncertain significance (Sep 22, 2022)
1-33864619-A-T		not specified	Uncertain significance (Jan 23, 2024)
1-33864654-G-A		not specified	Uncertain significance (Sep 29, 2023)
1-33864665-A-T		not specified	Uncertain significance (Feb 22, 2025)
1-33864721-G-C		not specified	Uncertain significance (Aug 04, 2023)
1-33864738-G-C		not specified	Uncertain significance (Sep 25, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HMGB4	protein_coding	protein_coding	ENST00000522796	1	4317

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00435	0.447	125418	1	125	125544	0.000502

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.216	110	104	1.06	0.00000587	1204
Missense in Polyphen		34	37.291	0.91175		469
Synonymous	0.742	35	41.0	0.853	0.00000231	343
Loss of Function	-0.366	3	2.39	1.26	9.92e-8	35

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000767	0.000767
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000875	0.000865
Middle Eastern	0.000109	0.000109
South Asian	0.0000679	0.0000653
Other	0.000327	0.000327

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0735

Intolerance Scores

• loftool: 0.396
• rvis_EVS: 0.68
• rvis_percentile_EVS: 85.04

Haploinsufficiency Scores

• pHI: 0.0389
• hipred: N
• hipred_score: 0.123
• ghis: 0.412

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hmgb4

Gene ontology

• Biological process: activation of innate immune response;DNA recombination;chromatin remodeling;regulation of transcription by RNA polymerase II;regulation of signaling receptor activity;positive regulation of autophagy;developmental process;positive regulation of interleukin-6 production;positive regulation of tumor necrosis factor production;positive regulation of innate immune response;positive regulation of transcription by RNA polymerase II;positive regulation of interleukin-1 secretion;positive regulation of interleukin-1 beta secretion;cell chemotaxis;positive regulation of ERK1 and ERK2 cascade;positive regulation of NIK/NF-kappaB signaling;positive regulation of interferon-alpha secretion
• Cellular component: nuclear chromatin;nucleus;cytoplasm
• Molecular function: protein binding;transcription factor binding;DNA binding, bending