PRAMEF11

PRAME family member 11, the group of PRAME family

Basic information

Region (hg38): 1:12824605-12831410

Links

ENSG00000239810 ∙ NCBI:440560 ∙ ∙ HGNC:14086 ∙ Uniprot:O60813 ∙ 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 PRAMEF11 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRAMEF11 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			53	9		62
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	53	12	0

Variants in PRAMEF11

This is a list of pathogenic ClinVar variants found in the PRAMEF11 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-12824946-C-T		not specified	Uncertain significance (Dec 21, 2022)
1-12824959-C-A		not specified	Uncertain significance (Jun 17, 2024)
1-12824982-C-T		not specified	Uncertain significance (Oct 22, 2024)
1-12824994-T-G		not specified	Uncertain significance (Jun 29, 2023)
1-12825000-C-A		not specified	Uncertain significance (Jun 09, 2022)
1-12825017-C-G		not specified	Uncertain significance (Nov 08, 2021)
1-12825072-A-G		not specified	Uncertain significance (Dec 27, 2023)
1-12825079-C-G		not specified	Uncertain significance (May 11, 2022)
1-12825086-G-C		not specified	Likely benign (Oct 29, 2024)
1-12825087-C-G		not specified	Uncertain significance (Mar 31, 2024)
1-12825091-A-G		not specified	Likely benign (Feb 17, 2024)
1-12825111-C-T		not specified	Likely benign (Dec 28, 2022)
1-12825120-T-C		not specified	Uncertain significance (Sep 20, 2024)
1-12825126-G-A		not specified	Uncertain significance (Oct 19, 2024)
1-12825135-T-A		not specified	Uncertain significance (Jun 26, 2023)
1-12825156-T-C		not specified	Uncertain significance (Nov 28, 2023)
1-12825243-C-T		not specified	Uncertain significance (Sep 27, 2021)
1-12825244-A-G		not specified	Uncertain significance (May 24, 2024)
1-12825258-G-C		not specified	Uncertain significance (Jan 08, 2024)
1-12825265-T-A		not specified	Uncertain significance (Aug 13, 2021)
1-12825268-C-T		not specified	Likely benign (Jul 15, 2021)
1-12825288-A-G		not specified	Uncertain significance (Jun 16, 2024)
1-12825301-C-A		not specified	Uncertain significance (Dec 06, 2022)
1-12825324-G-A		not specified	Uncertain significance (May 26, 2024)
1-12825342-A-G		not specified	Uncertain significance (Aug 13, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PRAMEF11	protein_coding	protein_coding	ENST00000436041	1	605

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-2.59	92	43.8	2.10	0.00000209	565
Missense in Polyphen		24	14.735	1.6288		187
Synonymous	-3.33	35	17.4	2.02	9.43e-7	159
Loss of Function

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.255

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0239

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