ZC3H4

protein-coding

zinc finger CCCH-type containing 4, the group of Zinc fingers CCCH-type|Armadillo like helical domain containing

Gene summary

This gene encodes a member of a family of CCCH (C-x8-C-x5-C-x3-H type) zinc finger domain-containing proteins. These zinc finger domains, which coordinate zinc finger binding and are characterized by three cysteine residues and one histidine residue, are nucleic acid-binding. Other family members are known to function in post-transcriptional regulation. [provided by RefSeq, Aug 2011]

Previous symbols:

C19orf7

MANE transcript

NM_015168.2

Inheritance

—

ClinVar variants

U:215B:39

Top phenotype

ZC3H4-related disorder

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chr19:47,064,187-47,113,776

External References & Databases

Ensembl (ENSG00000130749)

Transcript & Mutation Effects

hg38 • Region Span ~49.6 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 ZC3H4 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 208

ZC3H4-related disorderTotal: 35

not providedTotal: 15

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_015168.2. 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			6 clinvar	13 clinvar	11 clinvar	30
missense			203 clinvar	14 clinvar	1 clinvar	218
nonsense			1 clinvar			1
start loss						0
frameshift			2 clinvar			2
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	215	27	12	254

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 16 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_015168.2	RefSeq	NP_055983.1	14	MANE Select
ENST00000253048.10	Ensembl	ENSP00000253048.4	14	MANE Select
ENST00000601973.1	Ensembl	ENSP00000469684.1	8	Standard
XM_005258676.4	RefSeq	XP_005258733.1	14	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

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

Molecular Function

DNA-binding transcription factor activity, RNA polymerase II-specific
RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding
DNA-binding transcription factor activity
RNA binding
metal ion binding

Cellular Component

nucleus
nucleoplasm
cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000253048
Coding exons: 14
Length: 49566
Individuals with no LoFs: 124783
Homozygous LoFs: 0
Heterozygous LoFs: 7
Defined: 124790
p: 0.0000280

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.656	746	798	0.935	0.0000542	8378
Missense (PolyPhen)		95	115.73	0.8209		1145
Synonymous	-4.37	446	343	1.30	0.0000253	2661
Loss of Function	6.85	0	54.6	0.00	0.00000377	543

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000085	0.000065	rare
Latino/Admixed American	0.000035	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000064	0.000035	rare
South Asian	0.000066	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.0635
RVIS EVS: -1.32
RVIS percentile EVS: 4.78

Essentials

Essential (CRISPR): E
Essential (CRISPR2): S
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.582

Gene Damage Prediction

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