PRDM2

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

Basic information

Region (hg38): 1:13700187-13825079

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.

• Inborn genetic diseases (73 variants)
• not provided (6 variants)
• not specified (1 variants)
• Low bone mineral density (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.

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				2		2
missense			69	5	2	76
nonsense						0
start loss						0
frameshift						0
inframe indel				1	1	2
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	69	8	3

Variants in PRDM2

This is a list of pathogenic ClinVar variants found in the PRDM2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-13731019-C-T		not specified	Likely benign (Apr 01, 2022)
1-13732859-A-G		not specified	Uncertain significance (Jul 25, 2023)
1-13773089-T-C		not specified	Uncertain significance (Jan 02, 2024)
1-13773102-A-T		not specified	Uncertain significance (Jun 13, 2022)
1-13773141-C-T		not specified	Uncertain significance (Feb 28, 2023)
1-13773165-C-G		not specified	Uncertain significance (Apr 25, 2023)
1-13773182-G-A		not specified	Uncertain significance (Jul 21, 2022)
1-13773182-G-T		not specified	Uncertain significance (Feb 27, 2024)
1-13778502-C-G		not specified	Uncertain significance (Jan 30, 2024)
1-13778549-C-T		not specified	Uncertain significance (Jun 24, 2022)
1-13778567-G-A		not specified	Uncertain significance (Dec 26, 2023)
1-13778568-C-T		not specified	Uncertain significance (Apr 27, 2023)
1-13778579-G-A		not specified	Uncertain significance (Nov 17, 2022)
1-13778692-G-A		not specified	Uncertain significance (Feb 27, 2023)
1-13778727-G-A		not specified	Uncertain significance (May 05, 2022)
1-13778734-T-A		not specified	Uncertain significance (Mar 24, 2023)
1-13778741-C-A		not specified	Uncertain significance (Sep 01, 2021)
1-13778774-T-G		not specified	Uncertain significance (Jun 11, 2021)
1-13778932-G-A		not specified	Uncertain significance (Jan 22, 2024)
1-13778951-G-A		not specified	Likely benign (Mar 16, 2022)
1-13779009-G-A		not specified	Uncertain significance (Sep 17, 2021)
1-13779023-C-T		not specified	Uncertain significance (May 26, 2023)
1-13779060-A-G		not specified	Uncertain significance (Feb 23, 2023)
1-13779093-G-A		not specified	Uncertain significance (Jan 23, 2023)
1-13779342-G-A		not specified	Uncertain significance (Nov 09, 2023)

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