PRDM7

PR/SET domain 7, the group of Zinc fingers C2H2-type|PR/SET domain family

Basic information

Region (hg38): 16:90056566-90092072

Links

ENSG00000126856 ∙ NCBI:11105 ∙ OMIM:609759 ∙ HGNC:9351 ∙ Uniprot:Q9NQW5 ∙ 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 PRDM7 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRDM7 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				1		1
missense			22	1		23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	2	0

Variants in PRDM7

This is a list of pathogenic ClinVar variants found in the PRDM7 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-90058358-A-G		not specified	Likely benign (Apr 22, 2024)
16-90060351-C-A		not specified	Uncertain significance (Apr 19, 2024)
16-90060406-T-G		not specified	Uncertain significance (May 11, 2022)
16-90060451-C-T		not specified	Uncertain significance (May 15, 2023)
16-90060462-A-G		not specified	Uncertain significance (Feb 16, 2023)
16-90060501-C-A		not specified	Uncertain significance (Jul 20, 2021)
16-90060544-A-G		not specified	Uncertain significance (Oct 04, 2022)
16-90060562-G-C		not specified	Uncertain significance (Dec 22, 2023)
16-90060590-C-G		not specified	Uncertain significance (Aug 03, 2022)
16-90060604-C-G		not specified	Uncertain significance (Jul 14, 2022)
16-90060606-C-T		not specified	Uncertain significance (Oct 10, 2023)
16-90060609-G-T		not specified	Uncertain significance (Jan 09, 2024)
16-90061495-C-T		not specified	Uncertain significance (Aug 01, 2022)
16-90061976-T-C		not specified	Uncertain significance (Jul 14, 2023)
16-90062016-C-T		not specified	Uncertain significance (Jan 03, 2022)
16-90062020-C-G		not specified	Uncertain significance (Nov 29, 2021)
16-90062048-C-T		not specified	Uncertain significance (Feb 11, 2022)
16-90062070-C-T		not specified	Uncertain significance (Jan 16, 2024)
16-90062416-C-A		not specified	Uncertain significance (Aug 12, 2022)
16-90062421-G-A		not specified	Likely benign (Mar 20, 2024)
16-90062468-A-G			Likely benign (Mar 01, 2023)
16-90063639-A-T		not specified	Uncertain significance (May 21, 2024)
16-90063668-G-A		not specified	Uncertain significance (May 24, 2024)
16-90063713-G-A		not specified	Uncertain significance (Jun 13, 2024)
16-90063746-T-C		not specified	Likely benign (Feb 06, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PRDM7	protein_coding	protein_coding	ENST00000449207	10	35507

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.37e-18	0.00400	125340	0	408	125748	0.00162

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.499	279	257	1.09	0.0000132	3242
Missense in Polyphen		87	64.22	1.3547		843
Synonymous	0.511	87	93.3	0.933	0.00000512	900
Loss of Function	-0.0963	26	25.5	1.02	0.00000142	286

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0207	0.0206
Ashkenazi Jewish	0.00	0.00
East Asian	0.000220	0.000217
Finnish	0.0000464	0.0000462
European (Non-Finnish)	0.000318	0.000316
Middle Eastern	0.000220	0.000217
South Asian	0.000425	0.000425
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable histone methyltransferase. {ECO:0000250}.
• Pathway: Lysine degradation - Homo sapiens (human);Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription (Consensus)

Recessive Scores

• pRec: 0.0597

Intolerance Scores

• loftool: 0.908
• rvis_EVS: 1.91
• rvis_percentile_EVS: 97.42

Haploinsufficiency Scores

• pHI: 0.0590
• hipred: N
• hipred_score: 0.153

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.310

Gene Damage Prediction

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

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;positive regulation of reciprocal meiotic recombination;histone H3-K4 methylation
• Cellular component: nucleus;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;protein binding;chromatin DNA binding;histone methyltransferase activity (H3-K4 specific);sequence-specific DNA binding