PRAMEF19

PRAME family member 19, the group of PRAME family

Basic information

Region (hg38): 1:13368431-13371947

Links

ENSG00000204480 ∙ NCBI:645414 ∙ ∙ HGNC:24908 ∙ Uniprot:Q5SWL8 ∙ 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 PRAMEF19 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRAMEF19 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			12			12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	0	0

Variants in PRAMEF19

This is a list of pathogenic ClinVar variants found in the PRAMEF19 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-13369193-C-T		not specified	Uncertain significance (Apr 27, 2023)
1-13369224-T-A		not specified	Uncertain significance (Feb 15, 2023)
1-13369236-C-T		not specified	Uncertain significance (Sep 26, 2023)
1-13369247-G-C		not specified	Uncertain significance (Nov 13, 2024)
1-13369336-T-A		not specified	Uncertain significance (Nov 18, 2022)
1-13369350-C-A		not specified	Uncertain significance (Jan 24, 2025)
1-13369351-C-T		not specified	Uncertain significance (Dec 27, 2022)
1-13369361-G-C		not specified	Uncertain significance (Mar 07, 2024)
1-13369405-C-A		not specified	Uncertain significance (Oct 29, 2024)
1-13369433-G-T		not specified	Uncertain significance (Jan 18, 2025)
1-13369485-C-T		not specified	Uncertain significance (Jan 31, 2025)
1-13369510-G-A		not specified	Uncertain significance (Jun 02, 2023)
1-13369519-C-T		not specified	Uncertain significance (Nov 10, 2024)
1-13369539-T-C		not specified	Uncertain significance (Feb 27, 2025)
1-13369602-T-A		not specified	Uncertain significance (Nov 10, 2024)
1-13369636-G-A		not specified	Uncertain significance (Mar 23, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PRAMEF19	protein_coding	protein_coding	ENST00000540591	3	3517

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0597	0.510	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.312	53	59.8	0.886	0.00000318	3104
Missense in Polyphen		17	19.196	0.8856		994
Synonymous	1.51	16	25.7	0.622	0.00000136	954
Loss of Function	-1.54	1	0.220	4.54	9.28e-9	130

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: 0.0595
• hipred: N
• hipred_score: 0.187
• ghis: 0.468

Essentials

• gene_indispensability_pred: N
• gene_indispensability_score: 0.0133

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Low	Low
Primary Immunodeficiency	Medium	Low	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