ZNG1A

protein-coding

Zn regulated GTPase metalloprotein activator 1A

Gene summary

Predicted to enable GTPase activity; zinc chaperone activity; and zinc ion binding activity. Involved in kidney development. Predicted to be located in nucleus. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

CBWD1

MANE transcript

NM_018491.5

Inheritance

—

ClinVar variants

U:86B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.72

Max pathogenic AF

—

Genomic locus

chr9:120,837-179,147

External References & Databases

Ensembl (ENSG00000172785)

Transcript & Mutation Effects

hg38 • Region Span ~58.3 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 ZNG1A variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 86

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_018491.5. 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						0
missense			82 clinvar	4 clinvar		86
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	86	4	0	90

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 89 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_018491.5	RefSeq	NP_060961.3	15	MANE Select
ENST00000356521.9	Ensembl	ENSP00000348915.4	15	MANE Select
NM_001145355.2	RefSeq	NP_001138827.1	15	Standard
NM_001145356.2	RefSeq	NP_001138828.1	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: ENST00000356521
Coding exons: 15
Length: 67939
Individuals with no LoFs: 125522
Homozygous LoFs: 0
Heterozygous LoFs: 49
Defined: 125571
p: 0.000195

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-2.00	206	140	1.48	0.00000649	2532
Missense (PolyPhen)		80	37.467	2.1352		758
Synonymous	-0.866	59	51.1	1.15	0.00000249	689
Loss of Function	0.999	11	15.2	0.724	6.39e-7	322

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00025	0.00025	rare
Latino/Admixed American	0.00029	0.00026	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.0010	0.00092	notable
Finnish	0	0.0	absent
European (Non-Finnish)	0.000056	0.000053	rare
South Asian	0.00048	0.00042	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0908

Essentials

Essential (CRISPR): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0106

Gene Damage Prediction

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