PROM2

protein-coding

prominin 2

Gene summary

This gene encodes a member of the prominin family of pentaspan membrane glycoproteins. The encoded protein localizes to basal epithelial cells and may be involved in the organization of plasma membrane microdomains. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2009]

MANE transcript

NM_001165978.3

Inheritance

—

ClinVar variants

U:158B:11

Top phenotype

EBV-positive nodal T- and NK-cell lymphoma

gnomAD constraint

pLI —, LoF o/e 0.63

Max pathogenic AF

—

Genomic locus

chr2:95,274,449-95,291,308

External References & Databases

Ensembl (ENSG00000155066)

Transcript & Mutation Effects

hg38 • Region Span ~16.9 kb

Loading mutation effect viewer...

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 PROM2 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 150

not providedTotal: 4

EBV-positive nodal T- and NK-cell lymphomaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001165978.3. 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	1 clinvar	6
missense			147 clinvar	9 clinvar		156
nonsense			3 clinvar			3
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	158	10	1	169

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 24 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001165978.3	RefSeq	NP_001159450.1	23	MANE Select
ENST00000317620.14	Ensembl	ENSP00000318270.9	23	MANE Select
NM_001165977.3	RefSeq	NP_001159449.1	23	Standard
NM_001321070.2	RefSeq	NP_001307999.1	16	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

positive regulation of protein phosphorylation
positive regulation of cell projection organization
regulation of GTPase activity
negative regulation of pinocytosis
regulation of clathrin-dependent endocytosis

Molecular Function

cholesterol binding

Cellular Component

integral component of plasma membrane
microvillus
cilium
cell surface
basolateral plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000317620
Coding exons: 23
Length: 16856
Individuals with no LoFs: 125549
Homozygous LoFs: 0
Heterozygous LoFs: 198
Defined: 125747
p: 0.000788

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.922	432	489	0.883	0.0000300	5303
Missense (PolyPhen)		174	185.2	0.93952		2164
Synonymous	0.146	215	218	0.987	0.0000139	1746
Loss of Function	2.36	30	47.6	0.630	0.00000228	505

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0014	0.0011	notable
Latino/Admixed American	0.00058	0.00058	rare
Ashkenazi Jewish	0.00052	0.00050	rare
East Asian	0.0065	0.0064	notable
Finnish	0.000047	0.000046	rare
European (Non-Finnish)	0.00027	0.00026	rare
South Asian	0.00021	0.00020	rare
Other	0.00018	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0927

Intolerance Scores

LoFtool: 0.824
RVIS EVS: -0.37
RVIS percentile EVS: 28.26

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.287

Gene Damage Prediction

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