HMGN5

protein-coding

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

Gene summary

This gene encodes a nuclear protein with similarities to the high mobility group proteins, HMG14 and HMG17, which suggests that this protein may function as a nucleosomal binding and transcriptional activating protein. [provided by RefSeq, Sep 2009]

Previous symbols:

NSBP1

MANE transcript

NM_030763.3

Inheritance

—

ClinVar variants

U:41B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.24

Max pathogenic AF

—

Genomic locus

chrX:81,113,699-81,201,913

External References & Databases

Ensembl (ENSG00000198157)

Transcript & Mutation Effects

hg38 • Region Span ~88.2 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to HMGN5 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 12

not providedTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_030763.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			4 clinvar		1 clinvar	5
missense			22 clinvar	3 clinvar	2 clinvar	27
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			15 clinvar			15
Total	0	0	41	3	3	47

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 50 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_030763.3	RefSeq	NP_110390.1	6	MANE Select
ENST00000358130.7	Ensembl	ENSP00000350848.2	6	MANE Select
ENST00000373250.7	Ensembl	ENSP00000362347.3	5	Standard
ENST00000430960.5	Ensembl	ENSP00000399626.1	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

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

Molecular Function

chromatin binding
RNA binding
nucleosomal DNA binding

Cellular Component

chromatin
nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000358130
Coding exons: 6
Length: 88242
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.151	74	70.4	1.05	0.00000461	1881
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

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