ZSWIM4

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

Basic information

Region (hg38): 19:13795443-13832254

Links

ENSG00000132003 ∙ NCBI:65249 ∙ ∙ HGNC:25704 ∙ Uniprot:Q9H7M6 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ZSWIM4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZSWIM4 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				2	1	3
missense			53			53
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	53	2	1

Variants in ZSWIM4

This is a list of pathogenic ClinVar variants found in the ZSWIM4 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
19-13795724-G-A		not specified	Uncertain significance (Oct 18, 2021)
19-13795740-G-C		not specified	Uncertain significance (Dec 20, 2023)
19-13799738-C-T		not specified	Uncertain significance (May 03, 2023)
19-13799763-G-A		not specified	Uncertain significance (May 29, 2024)
19-13799768-G-A		not specified	Uncertain significance (May 23, 2023)
19-13799786-C-T		not specified	Uncertain significance (Nov 05, 2021)
19-13799804-T-C		not specified	Uncertain significance (Aug 30, 2021)
19-13799808-T-C		not specified	Uncertain significance (Jan 24, 2024)
19-13799856-G-T		not specified	Uncertain significance (Mar 19, 2024)
19-13799870-C-T		not specified	Uncertain significance (Feb 05, 2024)
19-13799894-G-A		not specified	Uncertain significance (Jan 04, 2024)
19-13804813-T-C		not specified	Uncertain significance (Apr 12, 2024)
19-13804818-G-A		not specified	Uncertain significance (Jun 22, 2023)
19-13804845-C-T		not specified	Uncertain significance (Apr 13, 2023)
19-13804879-G-A		not specified	Uncertain significance (Jun 09, 2022)
19-13804893-G-C		not specified	Uncertain significance (Jan 03, 2022)
19-13805008-C-T		not specified	Uncertain significance (Jun 13, 2024)
19-13805026-G-C		not specified	Uncertain significance (Aug 12, 2021)
19-13805073-A-C		not specified	Uncertain significance (Sep 14, 2022)
19-13805098-G-A		not specified	Uncertain significance (Mar 15, 2024)
19-13808868-G-A		not specified	Uncertain significance (Jan 26, 2023)
19-13808868-G-C		not specified	Uncertain significance (Jan 04, 2024)
19-13808940-G-A		not specified	Uncertain significance (Aug 12, 2021)
19-13808981-C-G		not specified	Uncertain significance (Sep 01, 2021)
19-13809070-G-A		not specified	Uncertain significance (Mar 04, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZSWIM4	protein_coding	protein_coding	ENST00000254323	13	36771

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000792	1.00	125645	0	103	125748	0.000410

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.29	470	632	0.744	0.0000453	6273
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000312	0.0000312
Ashkenazi Jewish	0.00700	0.00667
East Asian	0.0000544	0.0000544
Finnish	0.0000465	0.0000462
European (Non-Finnish)	0.000266	0.000255
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.000701	0.000652

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.412
• rvis_EVS: -1.32
• rvis_percentile_EVS: 4.76

Haploinsufficiency Scores

• pHI: 0.247
• hipred: Y
• hipred_score: 0.627
• ghis: 0.593

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.840

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zswim4

Gene ontology

• Biological process: regulation of axon guidance
• Cellular component: Cul2-RING ubiquitin ligase complex
• Molecular function: zinc ion binding