ZNF655

protein-coding

zinc finger protein 655, the group of Zinc fingers C2H2-type

Gene summary

This gene encodes a zinc finger protein. The zinc finger proteins are involved in DNA binding and protein-protein interactions. Multiple alternatively spliced transcript variants encoding distinct isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

MANE transcript

NM_138494.3

Inheritance

—

ClinVar variants

U:72B:7

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.26

Max pathogenic AF

—

Genomic locus

chr7:99,558,406-99,576,453

External References & Databases

Ensembl (ENSG00000197343)

Transcript & Mutation Effects

hg38 • Region Span ~18.0 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 ZNF655 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 78

not providedTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_138494.3. 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
missense			72 clinvar	4 clinvar	1 clinvar	77
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	72	6	1	79

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 101 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_138494.3	RefSeq	NP_612503.1	2	MANE Select
ENST00000252713.9	Ensembl	ENSP00000252713.4	2	MANE Select
NM_001009958.1	RefSeq	NP_001009958.1	2	Standard
NM_001009960.1	RefSeq	NP_001009960.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Retinoblastoma (RB) in Cancer
Gene expression (Transcription)
Generic Transcription Pathway
RNA Polymerase II Transcription

Biological Process

regulation of transcription by RNA polymerase II
negative regulation of G1/S transition of mitotic cell cycle

Molecular Function

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

Cellular Component

nucleus
nucleolus
cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000424881
Coding exons: 3
Length: 18048
Individuals with no LoFs: 125699
Homozygous LoFs: 0
Heterozygous LoFs: 48
Defined: 125747
p: 0.000191

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.661	235	265	0.886	0.0000121	3537
Missense (PolyPhen)		5	9.8197	0.50918		117
Synonymous	1.27	81	96.9	0.836	0.00000485	881
Loss of Function	2.98	5	19.0	0.262	8.60e-7	282

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.00014	0.00014	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00027	0.00027	rare
Finnish	0.00014	0.00014	rare
European (Non-Finnish)	0.00028	0.00028	rare
South Asian	0.00010	0.000098	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

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

Recessive Scores

pRec: 0.112

Intolerance Scores

LoFtool: 0.368
RVIS EVS: 1
RVIS percentile EVS: 90.72

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.988

Gene Damage Prediction

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