PRDM13

protein-coding

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

Gene summary

Predicted to enable histone methyltransferase activity. Predicted to be involved in regulation of gene expression. Predicted to act upstream of or within negative regulation of transcription by RNA polymerase II and neurogenesis. Predicted to be active in nucleus. Implicated in pontocerebellar hypoplasia. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_021620.4

Inheritance

AD, AR

ClinVar variants

P:8U:378B:225

Top phenotype

Cerebellar dysfunction, impaired intellectual development, and hypogonadotropic hypogonadism

gnomAD constraint

pLI —, LoF o/e 0.2

Max pathogenic AF

—

Genomic locus

chr6:99,606,774-99,615,578

External References & Databases

Ensembl (ENSG00000112238)

Transcript & Mutation Effects

hg38 • Region Span ~8.8 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

North Carolina macular dystrophyLIMITED

Inheritance Pattern: AD

Disease ID:MONDO:0007630

Submitter: Franklin by Genoox

Two presumed unrelated families with North Carolina macular dystrophy (NCMD) were found to carry a a novel duplication in PRDM13 gene

North Carolina macular dystrophyDEFINITIVE

Inheritance Pattern: AD

Disease ID:MONDO:0007630

Submitter: G2P

pontocerebellar hypoplasia, IIA 17LIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0030890

Submitter: Ambry Genetics

cerebellar dysfunction, impaired intellectual development, and hypogonadotropic hypogonadismLIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0859229

Submitter: Ambry Genetics

progressive bifocal chorioretinal atrophySTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0010932

Submitter: PanelApp Australia

North Carolina macular dystrophyMODERATE

Inheritance Pattern: AD

Disease ID:MONDO:0007630

Submitter: Ambry Genetics

pontocerebellar hypoplasia, IIA 17STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0030890

Submitter: PanelApp Australia

cerebellar dysfunction, impaired intellectual development, and hypogonadotropic hypogonadismSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0859229

Submitter: PanelApp Australia

cerebellar dysfunction, impaired intellectual development, and hypogonadotropic hypogonadismLIMITED

Inheritance Pattern: Unknown

Disease ID:MONDO:0859229

Submitter: Labcorp Genetics (formerly Invitae)

Clinical Genomic Database (CGD)

Cerebellar dysfunction, impaired intellectual development, and hypogonadotropic hypogonadismAR

Manifestation: Craniofacial; Endocrine; Neurologic; Ophthalmologic

Intervention: Endocrine

Rationale: 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

Comments: 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

Refs: 5686965; 26507665; 30710461; 34730112; 35390279; 36243009

Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PRDM13 variants in ClinVar

8 Conditions Cataloged

not providedTotal: 583

Inborn genetic diseasesTotal: 124

not specifiedTotal: 105

PRDM13-related disorderTotal: 58

Retinal dystrophyTotal: 7

Pontocerebellar hypoplasia, IIA 17Total: 5

Cerebellar dysfunction, impaired intellectual development, and hypogonadotropic hypogonadismTotal: 4

North Carolina macular dystrophyTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_021620.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar	186 clinvar	4 clinvar	192
missense			361 clinvar	33 clinvar	2 clinvar	396
nonsense		2 clinvar	3 clinvar			5
start loss			1 clinvar			1
frameshift	3 clinvar	2 clinvar	9 clinvar			14
splice donor/acceptor (+/-2bp)	1 clinvar		2 clinvar			3
Total	4	4	378	219	6	611

Highest pathogenic variant AF is 0.000005477794

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 3 of 3 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_021620.4	RefSeq	NP_067633.2	4	MANE Select
ENST00000369215.5	Ensembl	ENSP00000358217.5	4	MANE Select
ENST00000369214.2	Ensembl	ENSP00000358216.2	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

negative regulation of transcription by RNA polymerase II
histone methylation
neurogenesis

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

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000369215
Coding exons: 4
Length: 8849
Individuals with no LoFs: 124763
Homozygous LoFs: 0
Heterozygous LoFs: 14
Defined: 124777
p: 0.0000561

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.423	353	376	0.939	0.0000173	4424
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.00018	0.00017	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0.000093	0.000093	rare
European (Non-Finnish)	0.000047	0.000044	rare
South Asian	0.000034	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.843

Gene Damage Prediction

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