PRDM9

PR/SET domain 9, the group of Lysine methyltransferases|PR/SET domain family|Zinc fingers C2H2-type

Basic information

Region (hg38): 5:23443586-23528093

Previous symbols: [ "MSBP3" ]

Links

ENSG00000164256 ∙ NCBI:56979 ∙ OMIM:609760 ∙ HGNC:13994 ∙ Uniprot:Q9NQV7 ∙ 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 PRDM9 gene.

• Genetic non-acquired premature ovarian failure (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRDM9 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				4	2	6
missense	2		45	9		56
nonsense	1					1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					9	9
Total	3	0	45	13	11

Highest pathogenic variant AF is 0.0000197

Variants in PRDM9

This is a list of pathogenic ClinVar variants found in the PRDM9 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-23509053-A-G		not specified	Uncertain significance (Jan 27, 2022)
5-23509088-G-A		not specified	Uncertain significance (Aug 12, 2021)
5-23509490-C-T			Benign (Dec 31, 2019)
5-23509570-A-G		not specified	Uncertain significance (May 03, 2023)
5-23509955-C-T		Genetic non-acquired premature ovarian failure	Pathogenic (May 14, 2021)
5-23509991-G-A		not specified	Uncertain significance (Sep 17, 2021)
5-23510000-G-T		not specified	Uncertain significance (May 14, 2024)
5-23510013-C-T		not specified	Uncertain significance (Apr 25, 2023)
5-23510049-AT-A			Benign (Jun 20, 2021)
5-23510049-ATT-A			Benign (Jun 21, 2021)
5-23510094-A-G			Benign (Nov 12, 2018)
5-23510212-G-T			Benign (Nov 12, 2018)
5-23517916-C-T		not specified	Uncertain significance (Jan 04, 2022)
5-23521026-A-T		not specified	Uncertain significance (Nov 30, 2021)
5-23521035-G-T		not specified	Uncertain significance (Apr 26, 2024)
5-23521103-C-T			Benign (Dec 31, 2019)
5-23521134-T-G		not specified	Uncertain significance (Jun 24, 2022)
5-23522263-C-T			Benign (Jun 21, 2021)
5-23522325-A-C		not specified	Uncertain significance (Nov 09, 2023)
5-23522357-G-T		not specified	Uncertain significance (Mar 25, 2024)
5-23522372-G-A		not specified	Uncertain significance (May 02, 2024)
5-23522375-G-A		not specified	Uncertain significance (May 27, 2022)
5-23522624-G-A		not specified	Uncertain significance (Dec 28, 2023)
5-23522641-T-G		Genetic non-acquired premature ovarian failure	Pathogenic (May 14, 2021)
5-23522660-T-A		not specified	Uncertain significance (Jan 23, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PRDM9	protein_coding	protein_coding	ENST00000296682	10	21443

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.83e-27	0.000151	125516	0	231	125747	0.000919

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.746	507	462	1.10	0.0000254	5781
Missense in Polyphen		103	116.4	0.88486		1397
Synonymous	-0.734	183	171	1.07	0.00000867	1637
Loss of Function	-0.0832	40	39.4	1.01	0.00000215	485

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00734	0.00702
Ashkenazi Jewish	0.00129	0.00129
East Asian	0.00104	0.000707
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000426	0.000422
Middle Eastern	0.00104	0.000707
South Asian	0.000490	0.000490
Other	0.000825	0.000815

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Histone methyltransferase that specifically trimethylates 'Lys-4' of histone H3 during meiotic prophase and is essential for proper meiotic progression. Does not have the ability to mono- and dimethylate 'Lys-4' of histone H3. H3 'Lys-4' methylation represents a specific tag for epigenetic transcriptional activation. Plays a central role in the transcriptional activation of genes during early meiotic prophase (By similarity). {ECO:0000250}.
• Pathway: Lysine degradation - Homo sapiens (human);Reproduction;PKMTs methylate histone lysines;Chromatin modifying enzymes;Meiotic recombination;Meiosis;Chromatin organization;Cell Cycle (Consensus)

Intolerance Scores

• loftool: 0.973
• rvis_EVS: 1.32
• rvis_percentile_EVS: 94.07

Haploinsufficiency Scores

• pHI: 0.0675
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: K
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0231

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Prdm9
• Phenotype: reproductive system phenotype; endocrine/exocrine gland phenotype; cellular phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: meiotic gene conversion;regulation of transcription by RNA polymerase II;positive regulation of reciprocal meiotic recombination;nucleosome positioning;histone H3-K4 methylation
• Cellular component: nucleus;nucleoplasm;chromosome
• 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;recombination hotspot binding;histone-lysine N-methyltransferase activity;chromatin DNA binding;histone methyltransferase activity (H3-K4 specific);sequence-specific DNA binding;transcription regulatory region DNA binding;metal ion binding