ZCCHC14

protein-coding

zinc finger CCHC-type containing 14, the group of Sterile alpha motif domain containing|Zinc fingers CCHC-type

Gene summary

Predicted to enable nucleic acid binding activity; phosphatidylinositol binding activity; and zinc ion binding activity. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_015144.3

Inheritance

—

ClinVar variants

U:160B:14

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.15

Max pathogenic AF

—

Genomic locus

chr16:87,406,246-87,493,024

External References & Databases

Ensembl (ENSG00000140948)

Transcript & Mutation Effects

hg38 • Region Span ~86.8 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 ZCCHC14 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 156

not providedTotal: 8

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_015144.3. 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 clinvar	4
missense			152 clinvar	8 clinvar	2 clinvar	162
nonsense			1 clinvar			1
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			6 clinvar			6
Total	0	0	160	10	4	174

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_015144.3	RefSeq	NP_055959.2	13	MANE Select
ENST00000671377.2	Ensembl	ENSP00000499622.1	13	MANE Select
ENST00000268616.10	Ensembl	ENSP00000268616.4	13	Standard
ENST00000268616.9	Ensembl	ENSP00000268616.4	13	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

nucleic acid binding
zinc ion binding
phosphatidylinositol binding

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000268616
Coding exons: 13
Length: 85800
Individuals with no LoFs: 125738
Homozygous LoFs: 0
Heterozygous LoFs: 10
Defined: 125748
p: 0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.813	531	586	0.906	0.0000367	6164
Missense (PolyPhen)		99	154.93	0.63899		1763
Synonymous	-4.17	348	262	1.33	0.0000197	1961
Loss of Function	4.59	5	33.8	0.148	0.00000168	403

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00021	0.00012	rare
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00013	0.00011	rare
Finnish	0.000047	0.000046	rare
European (Non-Finnish)	0.000029	0.000026	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.110

Intolerance Scores

LoFtool: 0.146
RVIS EVS: -1.28
RVIS percentile EVS: 5.17

Essentials

Essential (CRISPR): E
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.913

Gene Damage Prediction

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