ZNF180

protein-coding

zinc finger protein 180, the group of Zinc fingers C2H2-type

Gene summary

Zinc finger proteins have been shown to interact with nucleic acids and to have diverse functions. The zinc finger domain is a conserved amino acid sequence motif containing 2 specifically positioned cysteines and 2 histidines that are involved in coordinating zinc. Kruppel-related proteins form 1 family of zinc finger proteins. See MIM 604749 for additional information on zinc finger proteins.[supplied by OMIM, Jul 2002]

MANE transcript

NM_001278509.3

Inheritance

—

ClinVar variants

U:110B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.58

Max pathogenic AF

—

Genomic locus

chr19:44,474,428-44,500,524

External References & Databases

Ensembl (ENSG00000167384)

Transcript & Mutation Effects

hg38 • Region Span ~26.1 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 ZNF180 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 110

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001278509.3. 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			107 clinvar	2 clinvar		109
nonsense						0
start loss			2 clinvar			2
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	110	4	0	114

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 45 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001278509.3	RefSeq	NP_001265438.2	4	MANE Select
ENST00000592529.6	Ensembl	ENSP00000468021.1	4	MANE Select
NM_001278508.4	RefSeq	NP_001265437.2	4	Standard
NM_001288759.4	RefSeq	NP_001275688.2	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: ENST00000221327
Coding exons: 5
Length: 24723
Individuals with no LoFs: 125504
Homozygous LoFs: 1
Heterozygous LoFs: 243
Defined: 125748
p: 0.000971

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.209	346	357	0.969	0.0000167	4641
Missense (PolyPhen)		114	128.55	0.88682		1660
Synonymous	-1.57	143	121	1.18	0.00000561	1203
Loss of Function	1.97	15	25.8	0.582	0.00000116	353

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00080	0.00080	rare
Latino/Admixed American	0.00061	0.00061	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.0012	0.0012	notable
Finnish	0.00023	0.00023	rare
European (Non-Finnish)	0.0011	0.0011	notable
South Asian	0.0016	0.0015	notable
Other	0.0020	0.0020	notable

dbNSFP Gene Annotations

Source: dbNSFP

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

Intolerance Scores

LoFtool: 0.896
RVIS EVS: 1.16
RVIS percentile EVS: 92.6

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.269

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High