HMGN3

high mobility group nucleosomal binding domain 3, the group of Canonical high mobility group

Basic information

Region (hg38): 6:79201245-79234689

Previous symbols: [ "TRIP7" ]

Links

ENSG00000118418

∙ NCBI:9324 ∙ OMIM:604502 ∙ HGNC:12312 ∙ Uniprot:Q15651 ∙ 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 HMGN3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HMGN3 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				1 clinvar		1
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	0	1	0

Variants in HMGN3

This is a list of pathogenic ClinVar variants found in the HMGN3 region.

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

Position	Phenotype	Significance	ClinVar
6-79201695-C-T	not specified	Uncertain significance (Jan 14, 2025)	3858163
6-79201724-T-C	not specified	Likely benign (May 21, 2024)	3284501
6-79202122-T-C	not specified	Likely benign (Mar 06, 2023)	2465130
6-79202142-C-T	not specified	Uncertain significance (Jul 27, 2022)	2404441
6-79202313-G-C	not specified	Uncertain significance (Dec 19, 2022)	2336875
6-79202352-C-T	not specified	Uncertain significance (Jan 09, 2025)	3858162
6-79203623-G-A	not specified	Uncertain significance (Mar 07, 2023)	2456098
6-79208548-G-A	not specified	Uncertain significance (Jan 06, 2023)	3106286
6-79208548-G-C	not specified	Uncertain significance (Apr 13, 2023)	2510208
6-79214995-C-T	not specified	Uncertain significance (Feb 23, 2023)	2459689

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HMGN3	protein_coding	protein_coding	ENST00000344726	6	33445

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0578	0.874	125725	0	7	125732	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.761	36	51.4	0.701	0.00000251	631
Missense in Polyphen		18	22.302	0.80711		288
Synonymous	0.319	15	16.7	0.901	8.10e-7	182
Loss of Function	1.53	3	7.52	0.399	3.14e-7	104

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000560	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000353	0.0000352
Middle Eastern	0.0000560	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Binds to nucleosomes, regulating chromatin structure and consequently, chromatin-dependent processes such as transcription, DNA replication and DNA repair. Affects both insulin and glucagon levels and modulates the expression of pancreatic genes involved in insulin secretion. Regulates the expression of the glucose transporter SLC2A2 by binding specifically to its promoter region and recruiting PDX1 and additional transcription factors. Regulates the expression of SLC6A9, a glycine transporter which regulates the glycine concentration in synaptic junctions in the central nervous system, by binding to its transcription start site. May play a role in ocular development and astrocyte function (By similarity). {ECO:0000250}.;

Recessive Scores

pRec: 0.163

Intolerance Scores

loftool: 0.366
rvis_EVS: 0.08
rvis_percentile_EVS: 59.43

Haploinsufficiency Scores

pHI: 0.350
hipred: N
hipred_score: 0.332
ghis: 0.637

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 1.00

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Hmgn3
Phenotype: homeostasis/metabolism phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan);

Gene ontology

Biological process: chromatin organization;biological_process;positive regulation of transcription by RNA polymerase II;regulation of insulin secretion involved in cellular response to glucose stimulus
Cellular component: chromatin;nucleoplasm;cytosol
Molecular function: nucleosomal DNA binding;thyroid hormone receptor binding