PRAME

PRAME nuclear receptor transcriptional regulator, the group of PRAME family

Basic information

Region (hg38): 22:22547701-22559361

Previous symbols: [ "MAPE" ]

Links

ENSG00000185686 ∙ NCBI:23532 ∙ OMIM:606021 ∙ HGNC:9336 ∙ Uniprot:P78395 ∙ 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 PRAME gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRAME gene is commonly pathogenic or not.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					2	2
missense			43	4	2	49
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	43	4	4

Variants in PRAME

This is a list of pathogenic ClinVar variants found in the PRAME region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
22-22548084-A-G		not specified	Uncertain significance (Jan 09, 2025)
22-22548087-G-A		not specified	Uncertain significance (Aug 04, 2023)
22-22548113-A-G		not specified	Uncertain significance (Dec 10, 2024)
22-22548132-G-A		not specified	Uncertain significance (Feb 28, 2024)
22-22548171-G-A		not specified	Uncertain significance (Jan 03, 2024)
22-22548189-A-C		not specified	Uncertain significance (Sep 27, 2021)
22-22548220-C-A		not specified	Uncertain significance (Aug 13, 2021)
22-22548236-G-C		not specified	Uncertain significance (Apr 10, 2023)
22-22548293-T-C		not specified	Uncertain significance (Feb 06, 2024)
22-22548304-G-C		not specified	Uncertain significance (Apr 26, 2024)
22-22548334-A-G			Benign (Jun 29, 2018)
22-22548425-G-A		not specified	Likely benign (Oct 12, 2022)
22-22548453-C-T		not specified	Uncertain significance (Sep 27, 2024)
22-22548519-T-C		not specified	Uncertain significance (Jan 04, 2022)
22-22548519-T-G		not specified	Uncertain significance (Aug 13, 2021)
22-22548577-C-T		not specified	Likely benign (Dec 13, 2023)
22-22548581-A-G		not specified	Uncertain significance (Aug 30, 2022)
22-22548588-C-G		not specified	Uncertain significance (Dec 09, 2023)
22-22548593-G-A		not specified	Uncertain significance (Nov 08, 2022)
22-22548599-C-T		not specified	Uncertain significance (Nov 15, 2023)
22-22548630-G-C		not specified	Uncertain significance (Mar 17, 2023)
22-22548639-C-A		not specified	Likely benign (Jan 18, 2022)
22-22549823-C-T		not specified	Uncertain significance (Oct 11, 2024)
22-22549846-G-A		not specified	Uncertain significance (Nov 17, 2022)
22-22549883-G-A		not specified	Uncertain significance (Jun 23, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PRAME	protein_coding	protein_coding	ENST00000543184	4	11646

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.39e-7	0.491	125680	0	40	125720	0.000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.870	323	282	1.15	0.0000151	3314
Missense in Polyphen		58	56.331	1.0296		800
Synonymous	-1.17	135	119	1.14	0.00000657	1036
Loss of Function	0.846	12	15.6	0.769	0.00000102	149

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000241	0.000241
Ashkenazi Jewish	0.000464	0.000397
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000169	0.000158
Middle Eastern	0.000109	0.000109
South Asian	0.000314	0.000294
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Functions as a transcriptional repressor, inhibiting the signaling of retinoic acid through the retinoic acid receptors RARA, RARB and RARG. Prevents retinoic acid-induced cell proliferation arrest, differentiation and apoptosis. {ECO:0000269|PubMed:16179254}.

Recessive Scores

• pRec: 0.141

Intolerance Scores

• loftool: 0.769
• rvis_EVS: 0.27
• rvis_percentile_EVS: 70.64

Haploinsufficiency Scores

• pHI: 0.0334
• hipred: N
• hipred_score: 0.179

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 1.00

Gene Damage Prediction

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

Gene ontology

• Biological process: apoptotic process;positive regulation of cell population proliferation;cell differentiation;regulation of growth;negative regulation of apoptotic process;negative regulation of cell differentiation;negative regulation of transcription, DNA-templated;negative regulation of retinoic acid receptor signaling pathway
• Cellular component: nucleus;cytoplasm;plasma membrane
• Molecular function: protein binding;retinoic acid receptor binding