HMGXB4

protein-coding

HMG-box containing 4, the group of Non-canonical high mobility group

Gene summary

High mobility group (HMG) proteins are nonhistone chromosomal proteins. See HMG2 (MIM 163906) for additional information on HMG proteins.[supplied by OMIM, Nov 2010]

Previous symbols:

HMG2L1

MANE transcript

NM_001003681.3

Inheritance

—

ClinVar variants

U:60

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.21

Max pathogenic AF

—

Genomic locus

chr22:35,257,452-35,295,807

External References & Databases

Ensembl (ENSG00000100281)

Transcript & Mutation Effects

hg38 • Region Span ~38.4 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 HMGXB4 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 55

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001003681.3. 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			1 clinvar			1
missense			56 clinvar			56
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	60	0	0	60

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 13 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001003681.3	RefSeq	NP_001003681.1	10	MANE Select
ENST00000216106.6	Ensembl	ENSP00000216106.5	10	MANE Select
NM_001362972.2	RefSeq	NP_001349901.1	7	Standard
ENST00000418170.5	Ensembl	ENSP00000395532.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

endosome to lysosome transport
Wnt signaling pathway
negative regulation of Wnt signaling pathway

Molecular Function

DNA binding

Cellular Component

NURF complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000216106
Coding exons: 10
Length: 38356
Individuals with no LoFs: 125726
Homozygous LoFs: 0
Heterozygous LoFs: 21
Defined: 125747
p: 0.0000835

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.24	251	313	0.803	0.0000159	3886
Missense (PolyPhen)		70	118.06	0.5929		1436
Synonymous	1.02	109	123	0.883	0.00000654	1177
Loss of Function	3.85	6	27.9	0.215	0.00000153	380

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0.00024	0.00020	rare
East Asian	0.000060	0.000054	rare
Finnish	0.000098	0.000092	rare
European (Non-Finnish)	0.00012	0.00011	rare
South Asian	0.000037	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Negatively regulates Wnt/beta-catenin signaling during development. {ECO:0000250}.;

Recessive Scores

pRec: 0.110

Intolerance Scores

LoFtool: 0.550
RVIS EVS: -0.49
RVIS percentile EVS: 22.36

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.893

Gene Damage Prediction

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