PRAMEF4

protein-coding

PRAME family member 4, the group of PRAME family

Gene summary

Predicted to enable ubiquitin-like ligase-substrate adaptor activity. Predicted to be involved in proteasome-mediated ubiquitin-dependent protein catabolic process. Predicted to be located in acrosomal vesicle. Predicted to be part of Cul2-RING ubiquitin ligase complex. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001009611.4

Inheritance

—

ClinVar variants

U:106B:14

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.53

Max pathogenic AF

—

Genomic locus

chr1:12,879,212-12,886,201

External References & Databases

Ensembl (ENSG00000243073)

Transcript & Mutation Effects

hg38 • Region Span ~7.0 kb

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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 PRAMEF4 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 113

not providedTotal: 9

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001009611.4. 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				3 clinvar		3
missense			106 clinvar	10 clinvar		116
nonsense						0
start loss				1 clinvar		1
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	106	14	0	120

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 2 of 2 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001009611.4	RefSeq	NP_001009611.2	3	MANE Select
ENST00000235349.6	Ensembl	ENSP00000235349.5	3	MANE Select

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

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

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000235349
Coding exons: 3
Length: 6981
Individuals with no LoFs: 124868
Homozygous LoFs: 1
Heterozygous LoFs: 14
Defined: 124883
p: 0.0000601

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-3.70	390	231	1.68	0.0000119	3050
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00016	0.00016	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000071	0.000062	rare
South Asian	0.00013	0.00013	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.993
RVIS EVS: 3.53
RVIS percentile EVS: 99.48

Essentials

Essential (CRISPR): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

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