PRAMEF17

PRAME family member 17, the group of PRAME family

Basic information

Region (hg38): 1:13389632-13392629

Links

ENSG00000204479 ∙ NCBI:391004 ∙ ∙ HGNC:29485 ∙ Uniprot:Q5VTA0 ∙ 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 PRAMEF17 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRAMEF17 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			26	6		32
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	7	0

Variants in PRAMEF17

This is a list of pathogenic ClinVar variants found in the PRAMEF17 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-13390369-C-T		not specified	Uncertain significance (Oct 12, 2022)
1-13390370-G-C		not specified	Uncertain significance (Apr 07, 2023)
1-13390412-G-A		not specified	Uncertain significance (Nov 09, 2023)
1-13390441-A-G		not specified	Uncertain significance (Jul 25, 2023)
1-13390442-G-A		not specified	Uncertain significance (Dec 19, 2022)
1-13390462-G-A		not specified	Uncertain significance (Nov 11, 2024)
1-13390475-C-T		Inborn genetic diseases	Likely benign (Feb 15, 2023)
1-13390483-C-T		not specified	Uncertain significance (Sep 25, 2023)
1-13390485-C-G		not specified	Uncertain significance (Apr 12, 2023)
1-13390558-A-G		not specified	Likely benign (May 30, 2022)
1-13390568-A-G		not specified	Uncertain significance (Jul 25, 2023)
1-13390601-A-G		not specified	Likely benign (Mar 18, 2024)
1-13390670-G-A		Inborn genetic diseases	Uncertain significance (Feb 06, 2023)
1-13391946-G-A		not specified	Uncertain significance (Sep 01, 2021)
1-13391978-T-A			Likely benign (Nov 01, 2022)
1-13391981-C-G			Likely benign (Nov 01, 2022)
1-13391993-G-A		not specified	Uncertain significance (Sep 16, 2021)
1-13392000-A-G		Inborn genetic diseases	Uncertain significance (Apr 01, 2022)
1-13392031-C-G		not specified	Uncertain significance (Dec 03, 2024)
1-13392039-A-G		not specified	Uncertain significance (Dec 15, 2022)
1-13392141-C-G		not specified	Uncertain significance (Jun 21, 2021)
1-13392156-A-G		not specified	Likely benign (Aug 08, 2023)
1-13392158-A-G		not specified	Uncertain significance (May 31, 2023)
1-13392172-G-A			Likely benign (Sep 01, 2023)
1-13392177-G-C		not specified	Uncertain significance (Feb 27, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PRAMEF17	protein_coding	protein_coding	ENST00000376098	3	2998

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.32e-8	0.0367	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.427	133	120	1.11	0.00000574	3060
Missense in Polyphen		29	32.206	0.90045		868
Synonymous	-1.24	57	46.2	1.23	0.00000215	914
Loss of Function	-1.50	9	5.29	1.70	2.22e-7	135

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: 0.0265
• hipred: N
• hipred_score: 0.255

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0148

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