HMGN5

high mobility group nucleosome binding domain 5, the group of Canonical high mobility group

Basic information

Region (hg38): X:81113699-81201913

Previous symbols: [ "NSBP1" ]

Links

ENSG00000198157 ∙ NCBI:79366 ∙ OMIM:300385 ∙ HGNC:8013 ∙ Uniprot:P82970 ∙ 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 HMGN5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HMGN5 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			7	2	2	11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	2	3

Variants in HMGN5

This is a list of pathogenic ClinVar variants found in the HMGN5 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-81114704-T-G		not specified	Uncertain significance (Jan 22, 2024)
X-81115003-C-G			Benign (Apr 04, 2018)
X-81115177-A-T		not specified	Uncertain significance (Nov 09, 2023)
X-81116214-T-C		not specified	Uncertain significance (Nov 10, 2024)
X-81116269-G-T		not specified	Uncertain significance (Jul 06, 2021)
X-81116304-A-G		not specified	Likely benign (Jan 03, 2024)
X-81118462-C-T			Benign (Aug 15, 2018)
X-81118464-C-G		not specified	Uncertain significance (Jun 12, 2023)
X-81118476-G-A		not specified	Uncertain significance (Jul 06, 2021)
X-81118482-G-A			Benign (Jul 13, 2018)
X-81119798-A-G		not specified	Uncertain significance (Jul 08, 2021)
X-81119810-C-A			Likely benign (Dec 31, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HMGN5	protein_coding	protein_coding	ENST00000358130	6	88242

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.310	0.624	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.151	74	70.4	1.05	0.00000461	1881
Missense in Polyphen		7	7.7561	0.90252		194
Synonymous	1.03	16	22.2	0.722	0.00000155	434
Loss of Function	1.41	1	4.08	0.245	2.57e-7	88

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Preferentially binds to euchromatin and modulates cellular transcription by counteracting linker histone-mediated chromatin compaction. {ECO:0000250}.

Recessive Scores

• pRec: 0.0875

Intolerance Scores

• loftool: 0.285
• rvis_EVS: 0.88
• rvis_percentile_EVS: 88.96

Haploinsufficiency Scores

• pHI: 0.453
• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hmgn5
• Phenotype: respiratory system phenotype; normal phenotype; hematopoietic system 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); immune system phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: chromatin organization;regulation of transcription, DNA-templated;positive regulation of cell population proliferation;positive regulation of gene expression;negative regulation of apoptotic process;positive regulation of transcription, DNA-templated;negative regulation of cell cycle arrest
• Cellular component: chromatin;nucleus
• Molecular function: chromatin binding;RNA binding;nucleosomal DNA binding