PRAMEF2

PRAME family member 2, the group of PRAME family

Basic information

Region (hg38): 1:12857085-12861909

Links

ENSG00000120952 ∙ NCBI:65122 ∙ ∙ HGNC:28841 ∙ Uniprot:O60811 ∙ 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 PRAMEF2 gene.

• Inborn genetic diseases (35 variants)
• not provided (4 variants)
• not specified (2 variants)
• Bladder exstrophy-epispadias-cloacal extrophy complex (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRAMEF2 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				3		3
missense			36		1	37
nonsense				1		1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	36	5	1

Variants in PRAMEF2

This is a list of pathogenic ClinVar variants found in the PRAMEF2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-12859030-G-C			Likely benign (May 01, 2022)
1-12859056-G-C		not specified	Uncertain significance (May 05, 2023)
1-12859057-C-A		not specified	Uncertain significance (Apr 07, 2022)
1-12859057-C-T			Likely benign (Jan 01, 2024)
1-12859061-C-A		not specified	Uncertain significance (Dec 20, 2023)
1-12859090-C-T			Likely benign (Jan 01, 2024)
1-12859091-A-G			Likely benign (Jan 01, 2024)
1-12859719-T-A			Likely benign (Jan 01, 2024)
1-12859721-C-T		not specified	Uncertain significance (Feb 27, 2023)
1-12859722-G-A		not specified	Uncertain significance (Nov 22, 2023)
1-12859724-G-T		not specified	Uncertain significance (Aug 12, 2022)
1-12859726-T-A		not specified	Uncertain significance (Feb 09, 2022)
1-12859754-C-T			Likely benign (Jan 01, 2024)
1-12859755-C-G			Likely benign (Jan 01, 2024)
1-12859760-G-T			Likely benign (Jan 01, 2024)
1-12859763-T-A			Likely benign (Jan 01, 2024)
1-12859771-G-T			Likely benign (Jan 01, 2024)
1-12859779-T-C			Likely benign (Jan 01, 2024)
1-12859787-G-A			Likely benign (Jan 01, 2024)
1-12859794-G-A		not specified	Uncertain significance (Mar 31, 2023)
1-12859799-A-G		not specified	Uncertain significance (Feb 28, 2024)
1-12859817-T-C			Likely benign (Jan 01, 2024)
1-12859825-G-T		not specified	Uncertain significance (Jan 29, 2024)
1-12859826-A-G			Likely benign (Jan 01, 2024)
1-12859827-C-A		not specified	Uncertain significance (Apr 07, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PRAMEF2	protein_coding	protein_coding	ENST00000240189	3	4824

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.74e-10	0.0314	110879	248	14250	125377	0.0596

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-3.95	392	225	1.74	0.0000117	3003
Missense in Polyphen		87	60.158	1.4462		915
Synonymous	-4.51	158	100	1.57	0.00000570	906
Loss of Function	-0.645	13	10.7	1.21	4.72e-7	140

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0536	0.0497
Ashkenazi Jewish	0.0280	0.0280
East Asian	0.235	0.269
Finnish	0.0723	0.0738
European (Non-Finnish)	0.0476	0.0476
Middle Eastern	0.235	0.269
South Asian	0.0535	0.0537
Other	0.0511	0.0510

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.932
• rvis_EVS: 5.21
• rvis_percentile_EVS: 99.84

Haploinsufficiency Scores

• pHI: 0.0755
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0295

Gene Damage Prediction

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

Gene ontology

• Biological process: positive regulation of cell population proliferation;negative regulation of apoptotic process;negative regulation of cell differentiation;negative regulation of transcription, DNA-templated
• Cellular component: cytoplasm