ZSWIM5

zinc finger SWIM-type containing 5, the group of Zinc fingers SWIM-type

Basic information

Region (hg38): 1:45016398-45306209

Links

ENSG00000162415 ∙ NCBI:57643 ∙ OMIM:620132 ∙ HGNC:29299 ∙ Uniprot:Q9P217 ∙ 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 ZSWIM5 gene.

• Inborn genetic diseases (46 variants)
• Normal pregnancy (1 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZSWIM5 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						0
missense			45	1	1	47
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	45	1	1

Variants in ZSWIM5

This is a list of pathogenic ClinVar variants found in the ZSWIM5 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-45018464-C-T		not specified	Uncertain significance (Dec 01, 2023)
1-45018522-C-T		not specified	Uncertain significance (Jan 11, 2023)
1-45018585-T-C		not specified	Uncertain significance (Aug 17, 2022)
1-45018602-T-C		not specified	Uncertain significance (Jan 23, 2024)
1-45018610-G-T		not specified	Uncertain significance (Oct 26, 2022)
1-45018614-C-T		not specified	Uncertain significance (Feb 01, 2023)
1-45018728-C-T		not specified	Uncertain significance (Dec 07, 2023)
1-45018731-C-T		not specified	Uncertain significance (Mar 21, 2022)
1-45018732-G-A		not specified	Uncertain significance (May 31, 2023)
1-45018774-G-A		not specified	Uncertain significance (Mar 11, 2022)
1-45018776-C-T		not specified	Uncertain significance (Mar 14, 2023)
1-45018893-T-C		not specified	Uncertain significance (Sep 21, 2021)
1-45018974-G-A		not specified	Uncertain significance (Oct 03, 2022)
1-45018983-C-T		not specified	Uncertain significance (Nov 14, 2023)
1-45019184-C-T		not specified	Uncertain significance (Dec 04, 2023)
1-45019214-A-G		not specified	Uncertain significance (Apr 22, 2022)
1-45019299-T-A		not specified	Uncertain significance (Oct 04, 2022)
1-45020140-C-T		not specified	Uncertain significance (Aug 02, 2022)
1-45020678-C-T		not specified	Uncertain significance (Apr 25, 2023)
1-45034320-G-C		not specified	Uncertain significance (Sep 12, 2023)
1-45034372-G-A		not specified	Uncertain significance (Aug 22, 2023)
1-45034383-C-T		not specified	Uncertain significance (Jun 18, 2021)
1-45034393-G-A		not specified	Uncertain significance (Dec 20, 2023)
1-45034414-T-C		not specified	Uncertain significance (Apr 12, 2023)
1-45035694-G-A		not specified	Uncertain significance (Feb 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZSWIM5	protein_coding	protein_coding	ENST00000359600	14	289811

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0398	0.960	124765	0	33	124798	0.000132

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.32	471	635	0.741	0.0000348	7586
Missense in Polyphen		35	38.976	0.89799		425
Synonymous	2.68	199	253	0.786	0.0000127	2480
Loss of Function	5.10	14	54.8	0.256	0.00000322	565

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000521	0.000521
Ashkenazi Jewish	0.00	0.00
East Asian	0.000223	0.000223
Finnish	0.0000465	0.0000464
European (Non-Finnish)	0.0000976	0.0000971
Middle Eastern	0.000223	0.000223
South Asian	0.0000982	0.0000980
Other	0.000165	0.000165

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.106

Intolerance Scores

• loftool: 0.687
• rvis_EVS: -0.73
• rvis_percentile_EVS: 14.2

Haploinsufficiency Scores

• pHI: 0.657
• hipred: Y
• hipred_score: 0.626
• ghis: 0.563

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.131

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zswim5
• Phenotype: pigmentation phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Gene ontology

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