ZNF157

protein-coding

zinc finger protein 157, the group of Zinc fingers C2H2-type|Small nucleolar RNA protein coding host genes

Gene summary

This gene product is a likely zinc finger family transcription factor. It contains KRAB-A and KRAB-B domains that act as transcriptional repressors in related proteins, and multiple zinc finger DNA binding motifs and finger linking regions characteristic of the Kruppel family. This gene is part of a gene cluster on chromosome Xp11.23. [provided by RefSeq, Jul 2008]

MANE transcript

NM_003446.4

Inheritance

—

ClinVar variants

U:72B:9

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.76

Max pathogenic AF

—

Genomic locus

chrX:47,370,578-47,414,498

External References & Databases

Ensembl (ENSG00000147117)

Transcript & Mutation Effects

hg38 • Region Span ~43.9 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 ZNF157 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 55

not providedTotal: 8

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_003446.4. 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			3 clinvar	1 clinvar	4 clinvar	8
missense			63 clinvar	3 clinvar	1 clinvar	67
nonsense			3 clinvar			3
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	72	4	5	81

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 3 of 3 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_003446.4	RefSeq	NP_003437.2	4	MANE Select
ENST00000377073.4	Ensembl	ENSP00000366273.4	4	MANE Select
ENST00001087959.1	Ensembl	ENSP00000757765.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Gene expression (Transcription)
Generic Transcription Pathway
RNA Polymerase II Transcription

Biological Process

negative regulation of transcription by RNA polymerase II

Molecular Function

DNA-binding transcription factor activity, RNA polymerase II-specific
DNA binding
DNA-binding transcription factor activity
metal ion binding

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000377073
Coding exons: 4
Length: 43723
Individuals with no LoFs: 125712
Homozygous LoFs: 12
Heterozygous LoFs: 16
Defined: 125740
p: 0.000111

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.314	180	192	0.936	0.0000142	3347
Missense (PolyPhen)		55	61.902	0.88849		1155
Synonymous	0.513	59	64.2	0.919	0.00000446	921
Loss of Function	0.774	9	11.9	0.758	8.92e-7	253

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000078	0.000062	rare
Latino/Admixed American	0.00040	0.00032	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00036	0.00027	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000098	0.000070	rare
South Asian	0.000053	0.000033	rare
Other	0.00047	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May be involved in transcriptional regulation.;

Recessive Scores

pRec: 0.109

Intolerance Scores

LoFtool: 0.787
RVIS EVS: 0.2
RVIS percentile EVS: 67.19

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.149

Gene Damage Prediction

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