PROM2

prominin 2

Basic information

Region (hg38): 2:95274449-95291308

Links

ENSG00000155066 ∙ NCBI:150696 ∙ OMIM:617160 ∙ HGNC:20685 ∙ Uniprot:Q8N271 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PROM2 gene.

• not_specified (150 variants)
• not_provided (4 variants)
• EBV-positive_nodal_T-_and_NK-cell_lymphoma (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PROM2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001165978.3. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			4	1	1	6
missense			147	9		156
nonsense			3			3
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4			4
Total	0	0	158	10	1

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PROM2	protein_coding	protein_coding	ENST00000317620	23	16856

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
		125549	0	198	125747	0.000788

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.922	432	489	0.883	0.0000300	5303
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00195	0.00169
Ashkenazi Jewish	0.000522	0.000496
East Asian	0.00645	0.00638
Finnish	0.0000466	0.0000462
European (Non-Finnish)	0.000271	0.000264
Middle Eastern	0.00645	0.00638
South Asian	0.000205	0.000196
Other	0.000177	0.000163

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0927

Intolerance Scores

• loftool: 0.824
• rvis_EVS: -0.37
• rvis_percentile_EVS: 28.26

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.287

Gene Damage Prediction

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

Gene ontology

• 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;negative regulation of caveolin-mediated endocytosis
• Cellular component: integral component of plasma membrane;microvillus;cilium;cell surface;basolateral plasma membrane;apical plasma membrane;cytoplasmic vesicle;microvillus membrane;cell projection;microspike;membrane raft;ciliary membrane;extracellular exosome;prominosome
• Molecular function: cholesterol binding