ZNF606

protein-coding

zinc finger protein 606, the group of Zinc fingers C2H2-type

Gene summary

This gene encodes a zinc finger protein containing a Kruppel-associated box (KRAB) domain at its N-terminus, followed by contiguous C2H2 zinc finger motifs. The encoded protein is a nuclear protein that can act as a transcriptional repressor of growth factor-mediated signaling pathways in a reporter gene assay. This protein has been shown to interact with the SRY-box 9 gene product, and suppresses its transcriptional activity by inhibiting its DNA binding activity. Reduced expression of this gene promotes chondrocyte differentiation. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Dec 2016]

Previous symbols:

ZNF328

MANE transcript

NM_001348022.3

Inheritance

ClinVar variants

U:97B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.22

Max pathogenic AF

—

Genomic locus

chr19:57,977,076-58,003,349

External References & Databases

Ensembl (ENSG00000166704)

Transcript & Mutation Effects

hg38 • Region Span ~26.3 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

neuromyelitis opticaLIMITED

Inheritance Pattern: AD

Disease ID:MONDO:0019100

Submitter: Ambry Genetics

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ZNF606 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 94

not providedTotal: 7

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001348022.3. 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			2 clinvar	2 clinvar	3 clinvar	7
missense			95 clinvar	1 clinvar		96
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	97	3	3	103

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 25 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001348022.3	RefSeq	NP_001334951.1	6	MANE Select
ENST00000551380.7	Ensembl	ENSP00000446972.2	6	MANE Select
NM_001348023.3	RefSeq	NP_001334952.1	3	Standard
NM_001348024.3	RefSeq	NP_001334953.1	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

regulation of transcription by RNA polymerase II

Molecular Function

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

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000341164
Coding exons: 6
Length: 26297
Individuals with no LoFs: 125738
Homozygous LoFs: 0
Heterozygous LoFs: 10
Defined: 125748
p: 0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.19	352	421	0.836	0.0000202	5319
Missense (PolyPhen)		144	215.46	0.66834		2742
Synonymous	-1.13	161	144	1.12	0.00000713	1360
Loss of Function	4.05	7	31.5	0.222	0.00000133	434

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.00012	0.00012	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000026	0.000026	rare
South Asian	0.000068	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May act as a transcriptional repressor. {ECO:0000269|PubMed:15964554}.;

Recessive Scores

pRec: 0.0868

Intolerance Scores

LoFtool: 0.615
RVIS EVS: -0.82
RVIS percentile EVS: 11.94

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.616

Gene Damage Prediction

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