UBAP2

protein-coding

ubiquitin associated protein 2, the group of Small nucleolar RNA protein coding host genes

Gene summary

The protein encoded by this gene contains a UBA (ubiquitin associated) domain, which is characteristic of proteins that function in the ubiquitination pathway. This gene may show increased expression in the adrenal gland and lymphatic tissues. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2013]

MANE transcript

NM_001370062.2

Inheritance

—

ClinVar variants

U:182B:17

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.36

Max pathogenic AF

—

Genomic locus

chr9:33,921,693-34,049,388

External References & Databases

Ensembl (ENSG00000137073)

Transcript & Mutation Effects

hg38 • Region Span ~127.7 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 UBAP2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 177

not providedTotal: 5

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001370062.2. 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			3 clinvar	2 clinvar		5
missense			170 clinvar	13 clinvar	2 clinvar	185
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			8 clinvar			8
Total	0	0	182	15	2	199

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 114 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001370062.2	RefSeq	NP_001356991.2	28	MANE Select
ENST00000379238.7	Ensembl	ENSP00000368540.2	28	MANE Select
NM_001282530.2	RefSeq	NP_001269459.1	10	Standard
NM_001370059.2	RefSeq	NP_001356988.2	28	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

RNA binding
cadherin binding

Cellular Component

nucleus
cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000379238
Coding exons: 28
Length: 127257
Individuals with no LoFs: 125680
Homozygous LoFs: 0
Heterozygous LoFs: 68
Defined: 125748
p: 0.000270

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.110	628	620	1.01	0.0000334	7205
Missense (PolyPhen)		166	181.69	0.91363		2215
Synonymous	-0.498	259	249	1.04	0.0000146	2315
Loss of Function	4.68	23	63.2	0.364	0.00000316	711

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00025	0.00025	rare
Latino/Admixed American	0.00019	0.00017	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00027	0.00027	rare
Finnish	0.00060	0.00060	rare
European (Non-Finnish)	0.00027	0.00027	rare
South Asian	0.00020	0.00020	rare
Other	0.00049	0.00049	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0856

Intolerance Scores

LoFtool: 0.722
RVIS EVS: -0.94
RVIS percentile EVS: 9.39

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: E
Indispensability score: 0.654

Gene Damage Prediction

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