ZNF280C

protein-coding

zinc finger protein 280C, the group of Zinc fingers C2H2-type

Gene summary

This gene encodes a member of the zinc finger domain-containing protein family. This family member contains multiple Cys2-His2(C2H2)-type zinc finger domains, the most common type of zinc finger domain that self-folds to form a beta-beta-alpha structure that binds a zinc ion. [provided by RefSeq, Aug 2011]

Previous symbols:

SUHW3

MANE transcript

NM_017666.5

Inheritance

—

ClinVar variants

U:160B:8

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.04

Max pathogenic AF

—

Genomic locus

chrX:130,202,707-130,268,899

External References & Databases

Ensembl (ENSG00000056277)

Transcript & Mutation Effects

hg38 • Region Span ~66.2 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 ZNF280C variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 57

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_017666.5. 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			16 clinvar			16
missense			119 clinvar	8 clinvar		127
nonsense			7 clinvar			7
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			18 clinvar			18
Total	0	0	160	8	0	168

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 10 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_017666.5	RefSeq	NP_060136.1	18	MANE Select
ENST00000370978.9	Ensembl	ENSP00000360017.4	18	MANE Select
ENST00000447817.1	Ensembl	ENSP00000408521.1	13	Standard
ENST00000930023.1	Ensembl	ENSP00000600082.1	19	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

regulation of transcription, DNA-templated
regulation of transcription by RNA polymerase II

Molecular Function

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

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000370978
Coding exons: 18
Length: 66189
Individuals with no LoFs: 113705
Homozygous LoFs: 1
Heterozygous LoFs: 0
Defined: 113706
p: 0.00000440

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.55	190	260	0.730	0.0000189	4881
Missense (PolyPhen)		18	68.973	0.26097		1396
Synonymous	0.0892	87	88.1	0.988	0.00000647	1325
Loss of Function	4.39	1	24.4	0.0410	0.00000167	516

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000079	0.000066	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May function as a transcription factor.;

Intolerance Scores

LoFtool: 0.0852
RVIS EVS: -0.49
RVIS percentile EVS: 22.36

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0299

Gene Damage Prediction

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