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.

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.

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			53	3		56
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	54	3	0

Variants in PRDM4

This is a list of pathogenic ClinVar variants found in the PRDM4 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-107734244-T-A		not specified	Uncertain significance (Aug 17, 2022)
12-107734286-T-A		not specified	Uncertain significance (Nov 21, 2024)
12-107734307-G-A		not specified	Uncertain significance (Jul 15, 2021)
12-107734451-T-C		not specified	Uncertain significance (Feb 06, 2023)
12-107739386-G-A		not specified	Uncertain significance (Dec 20, 2023)
12-107739423-G-A		not specified	Uncertain significance (May 13, 2022)
12-107739526-C-G		not specified	Uncertain significance (Jun 12, 2023)
12-107739539-T-C		not specified	Uncertain significance (Jan 29, 2024)
12-107739545-T-C		not specified	Uncertain significance (Jul 25, 2024)
12-107740951-T-G		not specified	Uncertain significance (Jul 12, 2023)
12-107740957-T-C		not specified	Uncertain significance (Aug 02, 2021)
12-107741033-T-C		not specified	Uncertain significance (Jun 29, 2023)
12-107741117-T-C		not specified	Uncertain significance (Jul 14, 2021)
12-107741131-T-C		not specified	Uncertain significance (Dec 11, 2023)
12-107741209-T-C		not specified	Likely benign (Mar 15, 2024)
12-107741212-C-T		not specified	Uncertain significance (Sep 23, 2023)
12-107742241-C-T		not specified	Uncertain significance (Feb 01, 2023)
12-107742311-C-T		not specified	Uncertain significance (Aug 08, 2024)
12-107742343-C-T		not specified	Uncertain significance (Oct 12, 2021)
12-107743272-T-C		not specified	Uncertain significance (May 26, 2024)
12-107743282-T-A		not specified	Uncertain significance (Sep 17, 2021)
12-107744631-C-T		not specified	Uncertain significance (Dec 27, 2022)
12-107744632-G-A		not specified	Uncertain significance (Jul 16, 2024)
12-107746317-T-G		not specified	Uncertain significance (Aug 09, 2021)
12-107746337-C-T		not specified	Uncertain significance (Jan 23, 2024)

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
0.00132	0.998	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

Haploinsufficiency Scores

• pHI: 0.273
• hipred: Y
• hipred_score: 0.729
• ghis: 0.626

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

Mouse Genome Informatics

• Gene name: Prdm4
• Phenotype: growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); muscle phenotype; skeleton phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); normal phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); limbs/digits/tail phenotype; vision/eye phenotype

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