PRDM4

PR/SET domain 4, the group of PR/SET domain family|Zinc fingers C2H2-type

Basic information

Region (hg38): 12:107732871-107761272

Links

ENSG00000110851 ∙ NCBI:11108 ∙ OMIM:605780 ∙ HGNC:9348 ∙ Uniprot:Q9UKN5 ∙ 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 PRDM4 gene.

• not_specified (94 variants)
• not_provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRDM4 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000012406.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			1	2		3
missense			94	3		97
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4			4
Total	0	0	99	5	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PRDM4	protein_coding	protein_coding	ENST00000228437	11	28407

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
		125700	0	48	125748	0.000191

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.07	379	442	0.857	0.0000227	5310
Missense in Polyphen		103	156.98	0.65613		1915
Synonymous	-0.0687	158	157	1.01	0.00000801	1561
Loss of Function	3.14	10	27.9	0.358	0.00000134	363

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00124	0.00124
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000133	0.000132
Middle Eastern	0.0000544	0.0000544
South Asian	0.000139	0.000131
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May function as a transcription factor involved in cell differentiation.
• Pathway: Neurotrophin signaling pathway - Homo sapiens (human);Signal Transduction;Death Receptor Signalling;p75 NTR receptor-mediated signalling;p75(NTR)-mediated signaling;p75NTR negatively regulates cell cycle via SC1 (Consensus)

Recessive Scores

• pRec: 0.116

Intolerance Scores

• loftool: 0.272
• rvis_EVS: -1.35
• rvis_percentile_EVS: 4.56

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 0.789

Gene Damage Prediction

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

Gene ontology

• Biological process: transcription by RNA polymerase II;signal transduction;cell population proliferation;histone H4-R3 methylation;positive regulation of transcription by RNA polymerase II
• Cellular component: nucleus;cytoplasm;histone methyltransferase complex
• Molecular function: RNA polymerase II regulatory region sequence-specific DNA binding;RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription factor activity;protein binding;methyltransferase activity;zinc ion binding;chromatin DNA binding;sequence-specific DNA binding;histone methyltransferase binding