ZNF660

protein-coding

zinc finger protein 660, the group of Zinc fingers C2H2-type

Gene summary

This gene encodes a protein that contains multiple C2H2 zinc finger domains, and is located in a cluster of zinc-finger encoding genes on chromosome 3. Naturally-occurring readthrough transcription is observed between this gene and the downstream zinc finger protein 197 gene and is represented by GeneID:110354863. [provided by RefSeq, May 2017]

MANE transcript

NM_173658.4

Inheritance

—

ClinVar variants

U:47

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.95

Max pathogenic AF

—

Genomic locus

chr3:44,578,223-44,599,694

External References & Databases

Ensembl (ENSG00000144792)

Transcript & Mutation Effects

hg38 • Region Span ~21.5 kb

Loading mutation effect viewer...

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 ZNF660 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 46

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_173658.4. 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						0
missense			47 clinvar			47
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	47	0	0	47

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 12 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_173658.4	RefSeq	NP_775929.2	1	MANE Select
ENST00000322734.2	Ensembl	ENSP00000324605.2	1	MANE Select
ENST00000416644.5	Ensembl	ENSP00000405284.1	1	Standard
ENST00000441021.5	Ensembl	ENSP00000411996.1	1	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: ENST00000322734
Coding exons: 1
Length: 21472
Individuals with no LoFs: 124705
Homozygous LoFs: 3
Heterozygous LoFs: 1039
Defined: 125747
p: 0.00415

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.451	161	178	0.905	0.00000907	2212
Missense (PolyPhen)		67	70.541	0.9498		879
Synonymous	-0.201	62	60.0	1.03	0.00000288	584
Loss of Function	0.136	10	10.5	0.955	6.70e-7	154

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0012	0.0012	notable
Latino/Admixed American	0.0029	0.0029	notable
Ashkenazi Jewish	0.0011	0.0011	notable
East Asian	0.00033	0.00027	rare
Finnish	0.0028	0.0028	notable
European (Non-Finnish)	0.0071	0.0071	notable
South Asian	0.00049	0.00049	rare
Other	0.0047	0.0047	notable

dbNSFP Gene Annotations

Source: dbNSFP

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

Intolerance Scores

LoFtool: 0.701
RVIS EVS: -0.05
RVIS percentile EVS: 50.01

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.136

Gene Damage Prediction

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