PRDM10

PR/SET domain 10, the group of Zinc fingers C2H2-type|PR/SET domain family

Basic information

Region (hg38): 11:129899705-130002835

Links

ENSG00000170325 ∙ NCBI:56980 ∙ OMIM:618319 ∙ HGNC:13995 ∙ Uniprot:Q9NQV6 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Birt-Hogg-Dube syndrome 2 (Limited), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Birt-Hogg-Dube syndrome	AD	Oncologic	The condtiion involve an increased risk of a variety of neoplasms, and awareness may allow early detection and management of oncologic sequelae	Dermatologic; Oncologic	36440963

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PRDM10 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRDM10 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					3	3
missense			40	2	2	44
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	40	2	5

Variants in PRDM10

This is a list of pathogenic ClinVar variants found in the PRDM10 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-129902345-C-T		not specified	Uncertain significance (Aug 04, 2023)
11-129902351-C-T		not specified	Uncertain significance (Dec 08, 2023)
11-129902356-G-T		not specified	Uncertain significance (May 24, 2024)
11-129902498-C-T		not specified	Uncertain significance (Nov 08, 2022)
11-129902507-C-G		not specified	Uncertain significance (Aug 04, 2023)
11-129905664-T-C		not specified	Uncertain significance (Jun 13, 2024)
11-129905727-T-G		not specified	Uncertain significance (Mar 16, 2022)
11-129910517-T-C		not specified	Uncertain significance (Aug 02, 2021)
11-129910541-T-G			Likely benign (Dec 01, 2022)
11-129910559-A-G		not specified	Uncertain significance (Dec 17, 2021)
11-129910599-A-T			Benign (Jul 06, 2018)
11-129912108-C-G		not specified	Uncertain significance (Oct 13, 2023)
11-129912108-C-T		not specified	Uncertain significance (May 12, 2024)
11-129912185-A-G		not specified	Uncertain significance (Oct 17, 2023)
11-129914744-T-C		not specified	Uncertain significance (Feb 15, 2023)
11-129914772-C-T		not specified	Uncertain significance (Apr 04, 2023)
11-129914888-C-T		not specified	Uncertain significance (Oct 04, 2022)
11-129914980-C-G		not specified	Uncertain significance (Dec 21, 2023)
11-129915688-G-A		not specified	Uncertain significance (Jan 17, 2024)
11-129915730-G-A		not specified	Uncertain significance (Apr 28, 2022)
11-129915775-C-T		not specified	Uncertain significance (Aug 02, 2021)
11-129917224-G-A		not specified	Uncertain significance (Dec 04, 2023)
11-129918598-C-T		not specified	Uncertain significance (Jan 17, 2024)
11-129918648-C-T		not specified	Uncertain significance (Dec 21, 2022)
11-129923264-C-T			Uncertain significance (-)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PRDM10	protein_coding	protein_coding	ENST00000358825	21	103130

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.153	0.847	125725	0	23	125748	0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.28	465	711	0.654	0.0000439	7621
Missense in Polyphen		195	362.29	0.53825		3716
Synonymous	0.0254	287	288	0.998	0.0000189	2235
Loss of Function	5.61	15	63.1	0.238	0.00000354	656

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000122	0.000122
Ashkenazi Jewish	0.0000995	0.0000992
East Asian	0.000109	0.000109
Finnish	0.000231	0.000231
European (Non-Finnish)	0.0000800	0.0000791
Middle Eastern	0.000109	0.000109
South Asian	0.0000653	0.0000653
Other	0.000168	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in transcriptional regulation. {ECO:0000250}.

Intolerance Scores

• loftool: 0.185
• rvis_EVS: -0.01
• rvis_percentile_EVS: 52.36

Haploinsufficiency Scores

• pHI: 0.341
• hipred: Y
• hipred_score: 0.575
• ghis: 0.518

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.834

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Prdm10
• Phenotype: growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); 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)

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;regulation of gene expression;methylation
• Cellular component: nucleus;histone methyltransferase complex
• Molecular function: RNA polymerase II core promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;protein binding;methyltransferase activity;metal ion binding