ZNG1C

protein-coding

Zn regulated GTPase metalloprotein activator 1C

Gene summary

Predicted to enable zinc chaperone activity and zinc ion binding activity. Predicted to be involved in protein maturation. Predicted to be located in nucleus. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

CBWD3

MANE transcript

NM_201453.4

Inheritance

—

ClinVar variants

U:33B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.28

Max pathogenic AF

—

Genomic locus

chr9:68,232,003-68,300,035

External References & Databases

Ensembl (ENSG00000196873)

Transcript & Mutation Effects

hg38 • Region Span ~68.0 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 ZNG1C variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 31

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_201453.4. 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						0
missense			31 clinvar	1 clinvar		32
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	33	1	0	34

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 78 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_201453.4	RefSeq	NP_958861.2	15	MANE Select
ENST00000360171.11	Ensembl	ENSP00000353295.6	15	MANE Select
NM_001291821.2	RefSeq	NP_001278750.1	14	Standard
NM_001378113.1	RefSeq	NP_001365042.1	14	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

ATP binding

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000360171
Coding exons: 15
Length: 58533
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.218	41	45.1	0.909	0.00000212	2555
Missense (PolyPhen)		15	14.947	1.0036		766
Synonymous	-0.978	22	16.9	1.30	8.46e-7	701
Loss of Function	-0.643	8	6.26	1.28	3.14e-7	325

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
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

Recessive Scores

pRec: 0.0981

Essentials

Essential (CRISPR): E
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0932

Gene Damage Prediction

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