PRAMEF12

PRAME family member 12, the group of PRAME family

Basic information

Region (hg38): 1:12773737-12777906

Links

ENSG00000116726 ∙ NCBI:390999 ∙ ∙ HGNC:22125 ∙ Uniprot:O95522 ∙ 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 PRAMEF12 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRAMEF12 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		1
missense			32	3		35
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	32	4	0

Variants in PRAMEF12

This is a list of pathogenic ClinVar variants found in the PRAMEF12 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-12774917-T-G		not specified	Uncertain significance (Feb 02, 2024)
1-12774962-C-T		not specified	Uncertain significance (Jan 03, 2024)
1-12775009-T-C		not specified	Uncertain significance (Aug 12, 2021)
1-12775010-G-A		not specified	Uncertain significance (Jul 13, 2021)
1-12775043-G-C		not specified	Uncertain significance (Oct 26, 2021)
1-12775103-G-A		not specified	Likely benign (Nov 09, 2023)
1-12775144-G-A		not specified	Uncertain significance (Dec 18, 2023)
1-12775147-C-T		not specified	Uncertain significance (Jan 30, 2024)
1-12775566-A-T		not specified	Uncertain significance (Jun 23, 2023)
1-12775572-G-A		not specified	Uncertain significance (Nov 17, 2023)
1-12775647-G-A		not specified	Likely benign (Mar 31, 2023)
1-12775647-G-T		not specified	Uncertain significance (Mar 01, 2024)
1-12775662-G-C		not specified	Uncertain significance (Jun 17, 2022)
1-12775685-C-A		not specified	Uncertain significance (Mar 29, 2023)
1-12775690-G-T		not specified	Uncertain significance (Jun 11, 2021)
1-12775787-G-A		not specified	Uncertain significance (Aug 16, 2022)
1-12775795-C-G		not specified	Uncertain significance (May 16, 2024)
1-12775826-C-T		not specified	Uncertain significance (Jun 13, 2022)
1-12775840-G-T		not specified	Uncertain significance (Jan 26, 2022)
1-12775883-G-A		not specified	Uncertain significance (Dec 11, 2023)
1-12775918-G-T		not specified	Uncertain significance (Dec 09, 2023)
1-12775949-C-A		not specified	Uncertain significance (Aug 22, 2022)
1-12775962-T-A		not specified	Uncertain significance (Aug 22, 2023)
1-12776042-C-T		not specified	Uncertain significance (Oct 27, 2022)
1-12776081-G-A		not specified	Uncertain significance (May 24, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PRAMEF12	protein_coding	protein_coding	ENST00000357726	3	3066

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000527	0.694	125678	0	42	125720	0.000167

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.13	301	251	1.20	0.0000139	3115
Missense in Polyphen		171	144.09	1.1867		1938
Synonymous	-3.88	158	107	1.48	0.00000590	993
Loss of Function	0.948	8	11.5	0.698	6.62e-7	118

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000876	0.000874
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000265	0.0000264
Middle Eastern	0.0000544	0.0000544
South Asian	0.000131	0.000131
Other	0.00103	0.000978

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.803
• rvis_EVS: 1.16
• rvis_percentile_EVS: 92.65

Haploinsufficiency Scores

• pHI: 0.0579
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0824

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pramef12

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