HMG20B

high mobility group 20B, the group of Non-canonical high mobility group

Basic information

Region (hg38): 19:3572777-3579088

Links

ENSG00000064961 ∙ NCBI:10362 ∙ OMIM:605535 ∙ HGNC:5002 ∙ Uniprot:Q9P0W2 ∙ 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 HMG20B gene.

• not_specified (35 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HMG20B gene is commonly pathogenic or not. These statistics are base on transcript: NM_000006339.3. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			34	1		35
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	34	1	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HMG20B	protein_coding	protein_coding	ENST00000333651	9	6312

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.691	0.309	124635	0	3	124638	0.0000120

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.23	121	213	0.569	0.0000146	2023
Missense in Polyphen		24	72.736	0.32996		670
Synonymous	-0.964	104	92.2	1.13	0.00000665	598
Loss of Function	3.14	3	16.9	0.177	7.28e-7	201

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000183	0.0000177
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for correct progression through G2 phase of the cell cycle and entry into mitosis. Required for RCOR1/CoREST mediated repression of neuronal specific gene promoters.
• Pathway: Factors involved in megakaryocyte development and platelet production;HDACs deacetylate histones;Chromatin modifying enzymes;Hemostasis;Chromatin organization (Consensus)

Intolerance Scores

• loftool: 0.589
• rvis_EVS: -0.21
• rvis_percentile_EVS: 38.28

Haploinsufficiency Scores

• pHI: 0.547
• hipred: Y
• hipred_score: 0.629
• ghis: 0.637

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.980

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hmg20b

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;cell cycle;blood coagulation;histone deacetylation;negative regulation of protein sumoylation;skeletal muscle cell differentiation;positive regulation of neuron differentiation
• Cellular component: nucleoplasm;chromosome;nuclear body
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;histone deacetylase activity;protein binding;protein heterodimerization activity