PRDM7

protein-coding

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

Gene summary

This gene encodes a member of a family of proteins that may have roles in transcription and other nuclear processes. The encoded protein contains a KRAB (Kruppel-associated box) domain -A box and a SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain and may function as a histone methyltransferase. [provided by RefSeq, Aug 2013]

MANE transcript

NM_001098173.2

Inheritance

—

ClinVar variants

U:70B:9

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.02

Max pathogenic AF

—

Genomic locus

chr16:90,056,566-90,092,072

External References & Databases

Ensembl (ENSG00000126856)

Transcript & Mutation Effects

hg38 • Region Span ~35.5 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PRDM7 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 77

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001098173.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	6 clinvar		7
missense			69 clinvar	3 clinvar		72
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	70	9	0	79

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 10 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001098173.2	RefSeq	NP_001091643.1	10	MANE Select
ENST00000449207.8	Ensembl	ENSP00000396732.2	10	MANE Select
ENST00000564210.2	Ensembl	ENSP00000457667.1	3	Standard
ENST00000568473.5	Ensembl	ENSP00000455390.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Lysine degradation - Homo sapiens (human)
Gene expression (Transcription)
Generic Transcription Pathway
RNA Polymerase II Transcription

Biological Process

regulation of transcription by RNA polymerase II
positive regulation of reciprocal meiotic recombination
histone H3-K4 methylation

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

Cellular Component

nucleus
chromosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000449207
Coding exons: 10
Length: 35507
Individuals with no LoFs: 125340
Homozygous LoFs: 0
Heterozygous LoFs: 408
Defined: 125748
p: 0.00162

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.499	279	257	1.09	0.0000132	3242
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.020	0.020	notable
Latino/Admixed American	0.0011	0.0011	notable
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00022	0.00022	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00032	0.00032	rare
South Asian	0.00042	0.00042	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Probable histone methyltransferase. {ECO:0000250}.;

Recessive Scores

pRec: 0.0597

Intolerance Scores

LoFtool: 0.908
RVIS EVS: 1.91
RVIS percentile EVS: 97.42

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.310

Gene Damage Prediction

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