PRAMEF4

PRAME family member 4, the group of PRAME family

Basic information

Region (hg38): 1:12879212-12886201

Links

ENSG00000243073 ∙ NCBI:400735 ∙ ∙ HGNC:31971 ∙ Uniprot:O60810 ∙ 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 PRAMEF4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRAMEF4 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			57	8		65
nonsense						0
start loss				1		1
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	57	11	0

Variants in PRAMEF4

This is a list of pathogenic ClinVar variants found in the PRAMEF4 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-12879635-T-A		not specified	Uncertain significance (Aug 19, 2024)
1-12879653-C-T		not specified	Uncertain significance (Oct 07, 2024)
1-12879686-C-G		not specified	Uncertain significance (Jul 19, 2022)
1-12879689-C-T		not specified	Uncertain significance (Dec 14, 2021)
1-12879692-C-G		not specified	Conflicting classifications of pathogenicity (Feb 07, 2025)
1-12879701-G-A		not specified	Uncertain significance (Dec 21, 2023)
1-12879705-C-T		not specified	Uncertain significance (Aug 20, 2024)
1-12879708-C-T		not specified	Uncertain significance (Dec 20, 2024)
1-12879725-C-T		not specified	Uncertain significance (May 30, 2024)
1-12879728-G-A		not specified	Uncertain significance (Sep 25, 2023)
1-12879837-G-T		not specified	Uncertain significance (Oct 04, 2022)
1-12879839-T-G		not specified	Uncertain significance (Sep 22, 2022)
1-12879841-A-C		not specified	Uncertain significance (Jun 24, 2022)
1-12879848-C-T		not specified	Uncertain significance (Dec 10, 2024)
1-12879857-G-A		not specified	Uncertain significance (Feb 22, 2025)
1-12879870-C-T		not specified	Likely benign (Nov 09, 2023)
1-12879873-T-A		not specified	Uncertain significance (Jan 26, 2023)
1-12879912-G-C		not specified	Uncertain significance (Oct 26, 2021)
1-12879926-G-A		not specified	Likely benign (Nov 12, 2021)
1-12879930-C-A		not specified	Uncertain significance (Oct 05, 2023)
1-12879967-G-A			Likely benign (Feb 01, 2024)
1-12880038-G-A		not specified	Uncertain significance (Nov 21, 2024)
1-12880058-A-T		not specified	Uncertain significance (May 29, 2024)
1-12880062-C-T		not specified	Uncertain significance (Feb 27, 2023)
1-12880068-T-G		not specified	Uncertain significance (Feb 28, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PRAMEF4	protein_coding	protein_coding	ENST00000235349	3	6981

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.02e-11	0.00636	124868	1	14	124883	0.0000601

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-3.70	390	231	1.68	0.0000119	3050
Missense in Polyphen		107	65.654	1.6298		960
Synonymous	-2.53	118	87.9	1.34	0.00000416	891
Loss of Function	-1.49	14	9.14	1.53	3.90e-7	113

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.000164	0.000164
Finnish	0.00	0.00
European (Non-Finnish)	0.0000710	0.0000617
Middle Eastern	0.000164	0.000164
South Asian	0.000132	0.000131
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.993
• rvis_EVS: 3.53
• rvis_percentile_EVS: 99.48

Haploinsufficiency Scores

• pHI: 0.146
• hipred: N
• hipred_score: 0.255

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

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