PRAMEF20

PRAME family member 20, the group of PRAME family

Basic information

Region (hg38): 1:13410450-13421328

Previous symbols: [ "PRAMEF21" ]

Links

ENSG00000204478 ∙ NCBI:645425 ∙ ∙ HGNC:25224 ∙ Uniprot:Q5VT98 ∙ 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 PRAMEF20 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRAMEF20 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			9	1		10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	9	2	0

Variants in PRAMEF20

This is a list of pathogenic ClinVar variants found in the PRAMEF20 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-13416391-G-T		not specified	Uncertain significance (Oct 01, 2024)
1-13416419-C-T		not specified	Uncertain significance (Sep 17, 2021)
1-13416421-T-A		not specified	Uncertain significance (Aug 05, 2024)
1-13416437-T-C		not specified	Uncertain significance (Oct 12, 2022)
1-13416490-A-G		not specified	Likely benign (Jan 26, 2023)
1-13416542-G-A		not specified	Uncertain significance (Sep 06, 2022)
1-13416551-T-C		not specified	Uncertain significance (Oct 06, 2022)
1-13416553-G-A		not specified	Uncertain significance (Oct 01, 2024)
1-13416601-G-A		not specified	Uncertain significance (Mar 24, 2023)
1-13416634-C-T		not specified	Uncertain significance (Jan 03, 2025)
1-13416635-G-A		not specified	Uncertain significance (Mar 10, 2025)
1-13418237-C-C		not specified	Likely benign (Apr 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PRAMEF20	protein_coding	protein_coding	ENST00000316412	3	10897

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00302	0.379	124776	0	10	124786	0.0000401

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.520	55	45.2	1.22	0.00000252	3083
Missense in Polyphen		15	13.874	1.0812		1041
Synonymous	-0.557	22	18.9	1.16	9.82e-7	964
Loss of Function	-0.776	3	1.86	1.61	7.88e-8	114

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.0000570	0.0000533
Middle Eastern	0.000163	0.000163
South Asian	0.0000348	0.0000329
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• pHI: 0.0689
• ghis: 0.468

Essentials

• essential_gene_CRISPR: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.111

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pramef20

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