PRAMEF1

PRAME family member 1, the group of PRAME family

Basic information

Region (hg38): 1:12791397-12796628

Links

ENSG00000116721 ∙ NCBI:65121 ∙ ∙ HGNC:28840 ∙ Uniprot:O95521 ∙ 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 PRAMEF1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRAMEF1 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				1	2	3
missense			38	1	1	40
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	38	2	3

Variants in PRAMEF1

This is a list of pathogenic ClinVar variants found in the PRAMEF1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-12793241-C-G		not specified	Uncertain significance (Aug 13, 2021)
1-12793254-A-C			Benign (Oct 10, 2018)
1-12793292-C-T		not specified	Uncertain significance (Apr 26, 2024)
1-12793334-A-G		not specified	Uncertain significance (Oct 14, 2023)
1-12793457-C-T		not specified	Uncertain significance (Jan 23, 2023)
1-12793477-G-T		not specified	Uncertain significance (Jul 02, 2024)
1-12793480-C-T		not specified	Uncertain significance (May 18, 2022)
1-12793508-G-A		not specified	Uncertain significance (May 28, 2024)
1-12793928-C-G		not specified	Uncertain significance (Apr 05, 2023)
1-12793944-G-A		not specified	Uncertain significance (Jan 16, 2024)
1-12793948-T-C		not specified	Benign (Mar 29, 2016)
1-12793953-A-C		not specified	Uncertain significance (Feb 16, 2023)
1-12793956-A-G		not specified	Benign (Mar 29, 2016)
1-12793976-C-T		not specified	Uncertain significance (Jul 25, 2023)
1-12794022-G-A		not specified	Uncertain significance (Sep 13, 2023)
1-12794057-C-T		not specified	Uncertain significance (Jul 17, 2023)
1-12794068-A-G			Likely benign (Jul 01, 2023)
1-12794198-C-T		not specified	Uncertain significance (Dec 12, 2023)
1-12794199-C-T		not specified	Uncertain significance (Jun 24, 2022)
1-12794217-A-G		not specified	Uncertain significance (Sep 26, 2024)
1-12794233-A-G		not specified	Uncertain significance (Apr 12, 2022)
1-12794272-G-A		not specified	Uncertain significance (Nov 08, 2024)
1-12794278-G-T		not specified	Uncertain significance (Jan 26, 2023)
1-12794282-C-T		not specified	Uncertain significance (Aug 04, 2021)
1-12794300-C-T		not specified	Uncertain significance (Nov 10, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PRAMEF1	protein_coding	protein_coding	ENST00000332296	3	5232

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.22e-11	0.0125	125565	0	26	125591	0.000104

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-2.13	326	234	1.39	0.0000130	2965
Missense in Polyphen		79	61.129	1.2923		906
Synonymous	-3.35	140	97.8	1.43	0.00000542	903
Loss of Function	-1.03	14	10.4	1.35	4.54e-7	137

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000534	0.000521
Ashkenazi Jewish	0.0000994	0.0000993
East Asian	0.00	0.00
Finnish	0.000185	0.000185
European (Non-Finnish)	0.0000971	0.0000968
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.994
• rvis_EVS: 1.67
• rvis_percentile_EVS: 96.3

Haploinsufficiency Scores

• pHI: 0.0948
• hipred: N
• hipred_score: 0.255

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.101

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