PRDM13

PR/SET domain 13, the group of PR/SET domain family

Basic information

Region (hg38): 6:99606774-99615578

Links

ENSG00000112238 ∙ NCBI:59336 ∙ OMIM:616741 ∙ HGNC:13998 ∙ Uniprot:Q9H4Q3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• North Carolina macular dystrophy (Limited), mode of inheritance: AD
• cerebellar dysfunction, impaired intellectual development, and hypogonadotropic hypogonadism (Limited), mode of inheritance: AR
• pontocerebellar hypoplasia, IIA 17 (Limited), mode of inheritance: AR
• cerebellar dysfunction, impaired intellectual development, and hypogonadotropic hypogonadism (Limited), mode of inheritance: Unknown
• North Carolina macular dystrophy (Moderate), mode of inheritance: AD
• North Carolina macular dystrophy (Definitive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Cerebellar dysfunction, impaired intellectual development, and hypogonadotropic hypogonadism	AR	Endocrine	Individuals may have hypogonadotropic hypogonadism, and surveillance in adolescence related to sexual maturation is indicated, as is monitoring of bone mineral density in order to allow early detection and treatment of disease	Craniofacial; Endocrine; Neurologic; Ophthalmologic	5686965; 26507665; 30710461; 34730112; 35390279; 36243009
Macular dystrophy, retinal, 3 is caused by heterozygous tandem duplication of a cis-regulatory element region downstream of IRX1, which affects IRX1 and PRDM13 activity

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PRDM13 gene.

• Inborn genetic diseases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRDM13 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			3	136	7	146
missense			274	17	5	296
nonsense			2			2
start loss						0
frameshift	1		5			6
inframe indel			19	3	2	24
splice donor/acceptor (+/-2bp)			2			2
splice region			3	6		9
non coding			1	12		13
Total	1	0	306	168	14

Variants in PRDM13

This is a list of pathogenic ClinVar variants found in the PRDM13 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-99607026-G-A		Retinal dystrophy	Uncertain significance (Jan 01, 2022)
6-99607040-C-A		Inborn genetic diseases	Uncertain significance (Aug 12, 2024)
6-99607040-C-T			Benign (Jan 23, 2025)
6-99607041-G-C			Uncertain significance (Jun 27, 2022)
6-99607047-G-A			Uncertain significance (Aug 30, 2023)
6-99607047-G-T			Uncertain significance (Mar 19, 2022)
6-99607052-A-G			Likely benign (Jan 12, 2024)
6-99607054-C-T			Uncertain significance (May 25, 2022)
6-99607056-C-G		Inborn genetic diseases	Uncertain significance (Jun 07, 2024)
6-99607067-C-A			Uncertain significance (Apr 20, 2023)
6-99607068-G-T		Inborn genetic diseases	Uncertain significance (Aug 12, 2024)
6-99607089-C-T			Uncertain significance (Oct 15, 2024)
6-99607091-G-A			Likely benign (Jul 06, 2024)
6-99607091-G-T			Likely benign (Dec 19, 2023)
6-99607096-G-T			Uncertain significance (Jul 03, 2023)
6-99607097-C-T			Likely benign (Dec 17, 2023)
6-99607101-C-A			Uncertain significance (Feb 24, 2022)
6-99607102-G-T		Inborn genetic diseases	Uncertain significance (Jul 09, 2024)
6-99607104-C-G		Inborn genetic diseases	Uncertain significance (Nov 28, 2024)
6-99607106-C-G			Likely benign (Jan 06, 2025)
6-99607108-G-A			Uncertain significance (Nov 08, 2022)
6-99607127-C-T			Likely benign (Apr 26, 2022)
6-99607129-A-G			Uncertain significance (May 26, 2023)
6-99607139-G-A			Likely benign (Sep 15, 2022)
6-99607147-C-T			Likely benign (Jan 13, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PRDM13	protein_coding	protein_coding	ENST00000369215	4	8849

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.563	0.437	124763	0	14	124777	0.0000561

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.423	353	376	0.939	0.0000173	4424
Missense in Polyphen		95	124.7	0.76183		1434
Synonymous	-1.04	187	170	1.10	0.00000840	1560
Loss of Function	3.30	4	19.9	0.201	8.55e-7	239

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000184	0.000184
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000930	0.0000928
European (Non-Finnish)	0.0000466	0.0000441
Middle Eastern	0.00	0.00
South Asian	0.0000341	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in transcriptional regulation.

Haploinsufficiency Scores

• pHI: 0.852

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.843

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Prdm13
• Phenotype: vision/eye phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;histone methylation;neurogenesis
• Cellular component: nucleus
• Molecular function: RNA polymerase II regulatory region sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription factor activity;chromatin DNA binding;histone methyltransferase activity;sequence-specific DNA binding;metal ion binding