ZSWIM1

zinc finger SWIM-type containing 1, the group of Zinc fingers SWIM-type

Basic information

Region (hg38): 20:45881227-45885266

Previous symbols: [ "C20orf162" ]

Links

ENSG00000168612 ∙ NCBI:90204 ∙ ∙ HGNC:16155 ∙ Uniprot:Q9BR11 ∙ 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 ZSWIM1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZSWIM1 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			24			24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	0	0

Variants in ZSWIM1

This is a list of pathogenic ClinVar variants found in the ZSWIM1 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-45882662-A-G		not specified	Uncertain significance (Nov 13, 2023)
20-45882872-A-G		not specified	Uncertain significance (Jul 12, 2023)
20-45882944-G-A		not specified	Uncertain significance (Aug 21, 2023)
20-45882960-A-C		not specified	Uncertain significance (Jun 29, 2023)
20-45883152-A-T		not specified	Uncertain significance (Dec 07, 2021)
20-45883319-C-T		not specified	Uncertain significance (Aug 21, 2023)
20-45883427-A-G		not specified	Uncertain significance (Jan 30, 2024)
20-45883450-G-A		not specified	Uncertain significance (Jan 05, 2022)
20-45883534-A-T		not specified	Uncertain significance (Jan 30, 2024)
20-45883632-C-T		not specified	Uncertain significance (Nov 01, 2022)
20-45883652-C-T		not specified	Uncertain significance (Dec 17, 2021)
20-45883654-C-A		not specified	Uncertain significance (Jun 18, 2021)
20-45883665-C-G		not specified	Uncertain significance (Oct 03, 2022)
20-45883676-A-G		not specified	Uncertain significance (Dec 28, 2022)
20-45883803-G-A		not specified	Uncertain significance (Dec 06, 2022)
20-45883805-C-T		not specified	Uncertain significance (May 30, 2023)
20-45883821-C-T		not specified	Uncertain significance (May 27, 2022)
20-45883865-C-A		not specified	Uncertain significance (Mar 28, 2023)
20-45883934-G-A		not specified	Uncertain significance (Dec 02, 2021)
20-45883958-C-G		not specified	Uncertain significance (Sep 25, 2023)
20-45883983-G-A		not specified	Uncertain significance (Apr 13, 2022)
20-45884005-A-C		not specified	Uncertain significance (Aug 02, 2021)
20-45884015-A-C		not specified	Uncertain significance (Aug 30, 2022)
20-45884046-T-C		not specified	Uncertain significance (Feb 10, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZSWIM1	protein_coding	protein_coding	ENST00000372523	1	4040

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.13e-11	0.0249	122713	21	3013	125747	0.0121

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.22	214	270	0.792	0.0000145	3189
Missense in Polyphen		56	71.858	0.77932		837
Synonymous	-0.197	115	112	1.02	0.00000599	988
Loss of Function	-0.345	16	14.6	1.10	7.98e-7	155

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0112	0.0112
Ashkenazi Jewish	0.0235	0.0235
East Asian	0.0197	0.0197
Finnish	0.0150	0.0149
European (Non-Finnish)	0.0107	0.0107
Middle Eastern	0.0197	0.0197
South Asian	0.0159	0.0158
Other	0.0135	0.0136

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.757
• rvis_EVS: 0.37
• rvis_percentile_EVS: 75.43

Haploinsufficiency Scores

• pHI: 0.211
• hipred: N
• hipred_score: 0.170
• ghis: 0.456

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.683

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zswim1
• Phenotype: growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan)

Gene ontology

• Cellular component: nucleus
• Molecular function: zinc ion binding