PRDM11

PR/SET domain 11, the group of PR/SET domain family

Basic information

Region (hg38): 11:45095805-45235110

Links

ENSG00000019485 ∙ NCBI:56981 ∙ OMIM:616347 ∙ HGNC:13996 ∙ Uniprot:Q9NQV5 ∙ 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 PRDM11 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRDM11 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						0
missense						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	0	0	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PRDM11	protein_coding	protein_coding	ENST00000424263	6	132171

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.974	0.0264	125655	0	2	125657	0.00000796

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.13	234	288	0.813	0.0000174	3130
Missense in Polyphen		64	99.598	0.64258		1132
Synonymous	-0.0265	119	119	1.00	0.00000761	927
Loss of Function	3.73	2	20.0	0.0999	0.00000103	235

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000622	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000882	0.00000880
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in transcription regulation. {ECO:0000269|PubMed:25499759}.

Haploinsufficiency Scores

• pHI: 0.197
• hipred: Y
• hipred_score: 0.563
• ghis: 0.573

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0582

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Prdm11

Gene ontology

• Biological process: negative regulation of cell growth;methylation;regulation of MAPK cascade;negative regulation of transcription, DNA-templated;positive regulation of transcription, DNA-templated;regulation of cell cycle;positive regulation of fibroblast apoptotic process
• Cellular component: nucleus;cytosol
• Molecular function: RNA polymerase II regulatory region sequence-specific DNA binding;core promoter binding;chromatin binding;DNA-binding transcription factor activity;methyltransferase activity;chromatin DNA binding;sequence-specific DNA binding