PRAMEF6

PRAME family member 6, the group of PRAME family

Basic information

Region (hg38): 1:12938472-12947580

Links

ENSG00000232423 ∙ NCBI:440561 ∙ ∙ HGNC:30583 ∙ Uniprot:Q5VXH4 ∙ 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 PRAMEF6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRAMEF6 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						0
missense			16	6		22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	6	0

Variants in PRAMEF6

This is a list of pathogenic ClinVar variants found in the PRAMEF6 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-12938685-C-T		not specified	Uncertain significance (Oct 12, 2024)
1-12938736-C-T		not specified	Likely benign (Apr 07, 2022)
1-12938878-C-G		not specified	Likely benign (Aug 09, 2021)
1-12941009-C-T		not specified	Uncertain significance (Jun 24, 2022)
1-12941032-G-T		not specified	Likely benign (Sep 01, 2021)
1-12941078-G-T		not specified	Likely benign (Aug 23, 2021)
1-12941141-C-T		not specified	Uncertain significance (Jul 09, 2021)
1-12941189-T-C		not specified	Likely benign (Jan 10, 2023)
1-12941230-T-A		not specified	Uncertain significance (Jun 29, 2022)
1-12941249-C-G		not specified	Uncertain significance (Apr 06, 2024)
1-12941329-T-C		not specified	Uncertain significance (Feb 22, 2023)
1-12941351-G-T		not specified	Uncertain significance (Feb 15, 2023)
1-12941386-T-A		not specified	Uncertain significance (Jul 12, 2022)
1-12941390-G-C		not specified	Uncertain significance (May 24, 2023)
1-12941410-G-C		not specified	Uncertain significance (Apr 06, 2024)
1-12941419-T-A		not specified	Uncertain significance (May 09, 2023)
1-12941444-C-G		not specified	Uncertain significance (Feb 26, 2025)
1-12941461-T-A		not specified	Uncertain significance (Mar 01, 2023)
1-12941489-G-C		not specified	Uncertain significance (Feb 28, 2023)
1-12941506-C-A		not specified	Uncertain significance (Jul 13, 2021)
1-12941560-C-A		not specified	Uncertain significance (May 24, 2023)
1-12942398-T-G		not specified	Likely benign (Apr 28, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PRAMEF6	protein_coding	protein_coding	ENST00000376189	3	119571

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.61e-11	0.00298	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-2.20	107	59.2	1.81	0.00000290	2963
Missense in Polyphen		16	11.576	1.3822		891
Synonymous	-2.45	38	23.0	1.65	0.00000111	896
Loss of Function	-3.01	12	4.85	2.47	2.07e-7	115

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• pHI: 0.111
• hipred: N
• hipred_score: 0.255

Essentials

• essential_gene_CRISPR: 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