PRDM15

PR/SET domain 15, the group of PR/SET domain family|Zinc fingers C2H2-type

Basic information

Region (hg38): 21:41798224-41879482

Previous symbols: [ "ZNF298", "C21orf83" ]

Links

ENSG00000141956 ∙ NCBI:63977 ∙ OMIM:617692 ∙ HGNC:13999 ∙ Uniprot:P57071 ∙ 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 PRDM15 gene.

• Inborn genetic diseases (66 variants)
• not provided (11 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRDM15 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				7		7
missense		1	45	3		49
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			19	2		21
Total	0	1	64	12	0

Variants in PRDM15

This is a list of pathogenic ClinVar variants found in the PRDM15 region.

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

Position	Type	Phenotype	Significance	ClinVar
21-41801245-A-T		not specified	Uncertain significance (Nov 28, 2023)
21-41801274-G-A		not specified	Uncertain significance (Nov 08, 2022)
21-41801353-C-T		not specified	Uncertain significance (Nov 02, 2023)
21-41801360-C-T			Likely benign (Nov 01, 2022)
21-41801420-C-T			Likely benign (May 01, 2022)
21-41801451-G-C		not specified	Uncertain significance (Apr 05, 2023)
21-41801466-G-A		not specified	Uncertain significance (Dec 01, 2022)
21-41801469-T-A		not specified	Uncertain significance (Jan 03, 2024)
21-41801634-G-A		not specified	Uncertain significance (Nov 22, 2023)
21-41801656-T-A		not specified	Uncertain significance (Mar 21, 2023)
21-41801682-G-A		not specified	Uncertain significance (Oct 05, 2023)
21-41801698-T-G		not specified	Uncertain significance (Sep 14, 2023)
21-41802876-C-T		not specified	Uncertain significance (Dec 28, 2023)
21-41802888-C-T		not specified	Uncertain significance (Oct 03, 2022)
21-41804560-C-T		not specified	Uncertain significance (Apr 06, 2022)
21-41810300-C-T		not specified	Uncertain significance (Apr 12, 2022)
21-41810306-C-T		not specified	Uncertain significance (Feb 16, 2023)
21-41810310-G-A			Likely benign (Nov 01, 2022)
21-41810313-C-T			Likely benign (Oct 01, 2022)
21-41810809-C-T			Likely pathogenic (Jan 01, 2020)
21-41815707-G-A		not specified	Uncertain significance (Oct 06, 2021)
21-41815713-C-T		not specified	Uncertain significance (May 16, 2022)
21-41815763-C-G		not specified	Uncertain significance (Dec 07, 2021)
21-41815783-T-C		not specified	Uncertain significance (Feb 06, 2024)
21-41819611-C-T		not specified	Uncertain significance (Nov 15, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PRDM15	protein_coding	protein_coding	ENST00000269844	31	81207

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000822	1.00	125699	0	49	125748	0.000195

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.42	703	908	0.774	0.0000597	9893
Missense in Polyphen		171	304.74	0.56114		3035
Synonymous	0.0933	385	387	0.994	0.0000297	2834
Loss of Function	5.33	23	71.7	0.321	0.00000367	836

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000335	0.000333
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000272	0.000272
Finnish	0.0000929	0.0000924
European (Non-Finnish)	0.000214	0.000211
Middle Eastern	0.000272	0.000272
South Asian	0.000229	0.000229
Other	0.000490	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Sequence-specific DNA-binding transcriptional regulator. Plays a role as a molecular node in a transcriptional network regulating embryonic development and cell fate decision. Stimulates the expression of upstream key transcriptional activators and repressors of the Wnt/beta-catenin and MAPK/ERK pathways, respectively, that are essential for naive pluripotency and self-renewal maintenance of embryonic stem cells (ESCs). Specifically promotes SPRY1 and RSPO1 transcription activation through recognition and direct binding of a specific DNA sequence in their promoter regions. Involved in early embryo development (By similarity). Plays also a role in induced pluripotent stem cells (iPSCs) reprogramming (PubMed:28740264). {ECO:0000250|UniProtKB:E9Q8T2, ECO:0000269|PubMed:28740264}.
• Pathway: FOXA1 transcription factor network;Validated nuclear estrogen receptor alpha network (Consensus)

Recessive Scores

• pRec: 0.102

Intolerance Scores

• loftool: 0.720
• rvis_EVS: -2
• rvis_percentile_EVS: 1.73

Haploinsufficiency Scores

• pHI: 0.0747
• hipred: N
• hipred_score: 0.458
• ghis: 0.626

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: K
• gene_indispensability_pred: N
• gene_indispensability_score: 0.143

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Prdm15

Gene ontology

• Biological process: multicellular organism development;methylation;negative regulation of MAPK cascade;positive regulation of transcription by RNA polymerase II;positive regulation of canonical Wnt signaling pathway;regulation of stem cell division
• Cellular component: nucleus;nucleoplasm;nuclear body
• Molecular function: RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;methyltransferase activity;metal ion binding;promoter-specific chromatin binding