HMGXB3

protein-coding

HMG-box containing 3, the group of Non-canonical high mobility group

Gene summary

This gene is one of the non-canonical high mobility group (HMG) genes. The encoded protein contains an HMG-box domain found in DNA binding proteins such as transcription factors and chromosomal proteins. [provided by RefSeq, Aug 2011]

Previous symbols:

HMGX3

MANE transcript

NM_014983.3

Inheritance

—

ClinVar variants

U:181B:12

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.14

Max pathogenic AF

—

Genomic locus

chr5:150,000,046-150,053,142

External References & Databases

Ensembl (ENSG00000113716)

Transcript & Mutation Effects

hg38 • Region Span ~53.1 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

Tourette syndromeLIMITED

Inheritance Pattern: Unknown

Disease ID:MONDO:0007661

Submitter: Labcorp Genetics (formerly Invitae)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to HMGXB3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 178

not providedTotal: 13

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_014983.3. 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				2 clinvar	1 clinvar	3
missense			175 clinvar	6 clinvar	3 clinvar	184
nonsense			3 clinvar			3
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	181	8	4	193

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 44 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_014983.3	RefSeq	NP_055798.3	19	MANE Select
ENST00000502717.6	Ensembl	ENSP00000421917.1	19	MANE Select
NM_001366501.2	RefSeq	NP_001353430.1	18	Standard
ENST00000503427.5	Ensembl	ENSP00000422231.1	20	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

regulation of transcription by RNA polymerase II
biological_process
phosphorylation

Molecular Function

DNA-binding transcription factor activity, RNA polymerase II-specific
DNA binding
kinase activity

Cellular Component

cellular_component
nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000502717
Coding exons: 19
Length: 52503
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	3.51	429	688	0.624	0.0000373	8331
Missense (PolyPhen)		126	268.58	0.46913		3360
Synonymous	3.15	211	278	0.760	0.0000155	2670
Loss of Function	5.70	7	50.9	0.138	0.00000253	649

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

Recessive Scores

pRec: 0.0844

Intolerance Scores

RVIS EVS: 1.67
RVIS percentile EVS: 96.29

Essentials

Essential (CRISPR): E
Essential (CRISPR2): S
Indispensability pred.: N
Indispensability score: 0.285

Gene Damage Prediction

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