ZNF10

protein-coding

zinc finger protein 10, the group of Zinc fingers C2H2-type

Gene summary

The protein encoded by this gene contains a C2H2 zinc finger, and has been shown to function as a transcriptional repressor. The Kruppel-associated box (KRAB) domain of this protein is found to be responsible for its transcriptional repression activity. RING finger containing protein TIF1 was reported to interact with the KRAB domain, and may serve as a mediator for the repression activity of this protein. [provided by RefSeq, Jul 2008]

MANE transcript

NM_015394.5

Inheritance

—

ClinVar variants

U:57B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.41

Max pathogenic AF

—

Genomic locus

chr12:133,130,575-133,159,465

External References & Databases

Ensembl (ENSG00000256223)

Transcript & Mutation Effects

hg38 • Region Span ~28.9 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 ZNF10 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 56

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_015394.5. 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						0
missense			57 clinvar	2 clinvar		59
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	57	2	0	59

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 38 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_015394.5	RefSeq	NP_056209.2	4	MANE Select
ENST00000248211.11	Ensembl	ENSP00000248211.6	4	MANE Select
ENST00000402932.2	Ensembl	ENSP00000384893.2	5	Standard
ENST00000402932.3	Ensembl	ENSP00000384893.2	5	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

regulation of transcription by RNA polymerase II

Molecular Function

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

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000248211
Coding exons: 4
Length: 28891
Individuals with no LoFs: 125728
Homozygous LoFs: 0
Heterozygous LoFs: 19
Defined: 125747
p: 0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.24	234	294	0.796	0.0000138	3819
Missense (PolyPhen)		69	106.83	0.64587		1384
Synonymous	0.119	100	102	0.985	0.00000454	1018
Loss of Function	2.43	8	19.6	0.407	8.89e-7	283

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.000065	0.000058	rare
Ashkenazi Jewish	0.00020	0.00020	rare
East Asian	0.00011	0.00011	rare
Finnish	0.000095	0.000092	rare
European (Non-Finnish)	0.000062	0.000062	rare
South Asian	0.000065	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

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

Recessive Scores

pRec: 0.0971

Intolerance Scores

RVIS EVS: -0.36
RVIS percentile EVS: 28.93

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.579

Gene Damage Prediction

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