ZSWIM4

protein-coding

zinc finger SWIM-type containing 4, the group of Zinc fingers SWIM-type

Gene summary

Predicted to enable zinc ion binding activity. Predicted to be part of Cul2-RING ubiquitin ligase complex. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001367834.3

Inheritance

—

ClinVar variants

U:149B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.37

Max pathogenic AF

—

Genomic locus

chr19:13,795,443-13,832,254

External References & Databases

Ensembl (ENSG00000132003)

Transcript & Mutation Effects

hg38 • Region Span ~36.8 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 ZSWIM4 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 142

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001367834.3. 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			1 clinvar	3 clinvar	1 clinvar	5
missense			144 clinvar	1 clinvar		145
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	149	4	1	154

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 26 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001367834.3	RefSeq	NP_001354763.1	14	MANE Select
ENST00000590508.6	Ensembl	ENSP00000468285.2	14	MANE Select
NM_023072.3	RefSeq	NP_075560.2	13	Standard
ENST00000254323.6	Ensembl	ENSP00000254323.2	13	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

regulation of axon guidance

Molecular Function

zinc ion binding

Cellular Component

Cul2-RING ubiquitin ligase complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000254323
Coding exons: 13
Length: 36771
Individuals with no LoFs: 125645
Homozygous LoFs: 0
Heterozygous LoFs: 103
Defined: 125748
p: 0.000410

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.29	470	632	0.744	0.0000453	6273
Missense (PolyPhen)		18	27.863	0.64602		203
Synonymous	1.14	264	289	0.914	0.0000219	2119
Loss of Function	3.61	14	38.0	0.368	0.00000181	410

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000031	0.000029	rare
Ashkenazi Jewish	0.0070	0.0067	notable
East Asian	0.000054	0.000054	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00027	0.00025	rare
South Asian	0	0.0	absent
Other	0.00070	0.00065	rare

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.412
RVIS EVS: -1.32
RVIS percentile EVS: 4.76

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.840

Gene Damage Prediction

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