HMG20A

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

Basic information

Region (hg38): 15:77420412-77485607

Links

ENSG00000140382 ∙ NCBI:10363 ∙ OMIM:605534 ∙ HGNC:5001 ∙ Uniprot:Q9NP66 ∙ 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 HMG20A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HMG20A 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			17	1		18
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	17	3	0

Variants in HMG20A

This is a list of pathogenic ClinVar variants found in the HMG20A region.

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

Position	Type	Phenotype	Significance	ClinVar
15-77458407-G-A		HMG20A-related disorder	Likely benign (Oct 28, 2019)
15-77458433-C-T			Likely benign (Jan 02, 2019)
15-77458439-C-T		not specified	Uncertain significance (Dec 15, 2023)
15-77458461-C-T		HMG20A-related disorder	Likely benign (Jul 19, 2019)
15-77464266-G-A		not specified	Uncertain significance (Mar 24, 2023)
15-77464326-A-G		not specified	Uncertain significance (Sep 01, 2021)
15-77467192-G-A		not specified	Uncertain significance (Jun 26, 2023)
15-77470943-C-T		not specified	Uncertain significance (Nov 03, 2023)
15-77470997-A-C		not specified	Uncertain significance (Jan 02, 2024)
15-77471014-C-G		not specified	Uncertain significance (May 30, 2024)
15-77471015-C-T		not specified	Uncertain significance (Mar 04, 2024)
15-77471797-G-A		not specified	Uncertain significance (Mar 19, 2024)
15-77477576-C-T		not specified	Uncertain significance (Jun 04, 2024)
15-77477577-G-A		not specified	Uncertain significance (Apr 10, 2023)
15-77477619-A-G		not specified	Uncertain significance (May 01, 2022)
15-77478372-G-A		not specified	Uncertain significance (Dec 03, 2021)
15-77478430-G-C		not specified	Uncertain significance (Nov 17, 2022)
15-77478468-C-T		not specified	Uncertain significance (Aug 10, 2021)
15-77478474-G-A		not specified	Uncertain significance (Sep 06, 2022)
15-77478492-G-A		not specified	Uncertain significance (May 04, 2022)
15-77479196-A-G		not specified	Uncertain significance (Dec 06, 2021)
15-77479254-C-A		not specified	Uncertain significance (Sep 12, 2023)
15-77479311-G-A		not specified	Uncertain significance (Aug 08, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HMG20A	protein_coding	protein_coding	ENST00000381714	8	65196

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.678	0.322	125727	0	7	125734	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.41	148	205	0.722	0.0000120	2295
Missense in Polyphen		23	54.252	0.42395		551
Synonymous	-0.167	70	68.2	1.03	0.00000339	641
Loss of Function	3.46	4	21.2	0.189	0.00000137	219

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000294	0.0000294
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000356	0.0000352
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in neuronal differentiation as chromatin- associated protein. Acts as inhibitor of HMG20B. Overcomes the repressive effects of the neuronal silencer REST and induces the activation of neuronal-specific genes. Involved in the recruitment of the histone methyltransferase KMT2A/MLL1 and consequent increased methylation of histone H3 lysine 4 (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.110

Intolerance Scores

• rvis_EVS: -0.16
• rvis_percentile_EVS: 41.64

Haploinsufficiency Scores

• pHI: 0.569
• hipred: Y
• hipred_score: 0.654
• ghis: 0.657

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.636

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hmg20a

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;chromatin organization;regulation of transcription, DNA-templated;negative regulation of protein sumoylation;negative regulation of neuron differentiation
• Cellular component: nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;DNA-binding transcription factor activity;protein binding;identical protein binding;protein heterodimerization activity