PRDM2

PR/SET domain 2, the group of PR/SET domain family|Lysine methyltransferases

Basic information

Region (hg38): 1:13700188-13825079

Links

ENSG00000116731

∙ NCBI:7799 ∙ OMIM:601196 ∙ HGNC:9347 ∙ Uniprot:Q13029 ∙ 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 PRDM2 gene.

not_specified (208 variants)
not_provided (6 variants)
Flexion_contracture (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRDM2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001393986.1. 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	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				6 clinvar		6
missense			198 clinvar	6 clinvar	2 clinvar	206
nonsense						0
start loss						0
frameshift		1 clinvar				1
splice donor/acceptor (+/-2bp)						0
Total	0	1	198	12	2

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PRDM2	protein_coding	protein_coding	ENST00000235372	8	124882

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000438	125718	0	30	125748	0.000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.08	845	938	0.900	0.0000515	11243
Missense in Polyphen		180	245.13	0.73431		2946
Synonymous	-2.06	415	365	1.14	0.0000217	3407
Loss of Function	6.29	7	59.3	0.118	0.00000350	752

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000187	0.000185
Ashkenazi Jewish	0.000198	0.000198
East Asian	0.000124	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000177	0.000167
Middle Eastern	0.000124	0.000109
South Asian	0.0000980	0.0000980
Other	0.000186	0.000163

dbNSFP

Source: dbNSFP

Function: FUNCTION: S-adenosyl-L-methionine-dependent histone methyltransferase that specifically methylates 'Lys-9' of histone H3. May function as a DNA-binding transcription factor. Binds to the macrophage-specific TPA-responsive element (MTE) of the HMOX1 (heme oxygenase 1) gene and may act as a transcriptional activator of this gene. {ECO:0000269|PubMed:14633678}.;
Pathway: Lysine degradation - Homo sapiens (human);Histone Modifications (Consensus)

Recessive Scores

pRec: 0.215

Intolerance Scores

loftool: 0.554
rvis_EVS: -0.55
rvis_percentile_EVS: 19.81

Haploinsufficiency Scores

pHI: 0.284
hipred: Y
hipred_score: 0.655
ghis: 0.575

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.730

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Prdm2
Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); neoplasm;

Gene ontology

Biological process: regulation of transcription, DNA-templated;determination of adult lifespan;histone lysine methylation;positive regulation of transcription by RNA polymerase II
Cellular component: nucleus;Golgi apparatus
Molecular function: RNA polymerase II regulatory region sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific;DNA-binding transcription factor activity;zinc ion binding;histone-lysine N-methyltransferase activity;chromatin DNA binding;sequence-specific DNA binding