ZSWIM2

zinc finger SWIM-type containing 2, the group of Ring finger proteins|Zinc fingers ZZ-type|Zinc fingers SWIM-type

Basic information

Region (hg38): 2:186827475-186849208

Links

ENSG00000163012 ∙ NCBI:151112 ∙ ∙ HGNC:30990 ∙ Uniprot:Q8NEG5 ∙ 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 ZSWIM2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZSWIM2 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			47	1	1	49
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	47	1	1

Variants in ZSWIM2

This is a list of pathogenic ClinVar variants found in the ZSWIM2 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-186828048-A-G		not specified	Uncertain significance (Jun 18, 2021)
2-186828052-G-T		not specified	Uncertain significance (Dec 06, 2022)
2-186828139-A-G		not specified	Uncertain significance (Jun 29, 2023)
2-186828141-T-C		not specified	Uncertain significance (May 13, 2024)
2-186828165-G-A		not specified	Uncertain significance (Mar 18, 2024)
2-186828219-T-C		not specified	Uncertain significance (Jun 06, 2023)
2-186828244-A-T		not specified	Uncertain significance (Feb 14, 2025)
2-186828258-C-T		not specified	Likely benign (May 15, 2024)
2-186828259-G-A		not specified	Uncertain significance (Mar 21, 2023)
2-186828330-T-C		not specified	Uncertain significance (Oct 08, 2024)
2-186828337-T-C		not specified	Uncertain significance (Jan 26, 2023)
2-186828376-A-G		not specified	Uncertain significance (Jan 14, 2025)
2-186828405-G-C		not specified	Uncertain significance (Jan 27, 2022)
2-186828490-T-C		not specified	Uncertain significance (Feb 07, 2025)
2-186828519-T-G		not specified	Uncertain significance (Feb 15, 2023)
2-186828523-G-T		not specified	Uncertain significance (Aug 11, 2022)
2-186828577-T-C		not specified	Uncertain significance (Apr 07, 2022)
2-186828582-T-A		not specified	Uncertain significance (Dec 27, 2023)
2-186828717-T-C		not specified	Uncertain significance (Feb 06, 2023)
2-186828733-C-A		not specified	Uncertain significance (Feb 04, 2025)
2-186828736-T-C		not specified	Uncertain significance (Nov 08, 2022)
2-186829753-T-C		not specified	Uncertain significance (Jan 30, 2024)
2-186829767-T-C		not specified	Uncertain significance (Dec 14, 2021)
2-186829791-C-T		not specified	Uncertain significance (Aug 19, 2024)
2-186829845-A-G		not specified	Uncertain significance (Jan 27, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZSWIM2	protein_coding	protein_coding	ENST00000295131	9	21374

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.84e-15	0.0424	125541	0	207	125748	0.000823

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.952	360	313	1.15	0.0000144	4169
Missense in Polyphen		84	80.171	1.0478		1051
Synonymous	0.513	105	112	0.938	0.00000520	1132
Loss of Function	0.548	24	27.1	0.886	0.00000122	378

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00447	0.00446
Ashkenazi Jewish	0.00	0.00
East Asian	0.00327	0.00327
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.000328	0.000316
Middle Eastern	0.00327	0.00327
South Asian	0.000500	0.000490
Other	0.00115	0.00114

dbNSFP

Source: dbNSFP

• Function: FUNCTION: E3 ubiquitin-protein ligase involved in the regulation of Fas-, DR3- and DR4-mediated apoptosis. Functions in conjunction with the UBE2D1, UBE2D3 and UBE2E1 E2 ubiquitin-conjugating enzymes. {ECO:0000250}.

Recessive Scores

• pRec: 0.0936

Intolerance Scores

• loftool: 0.635
• rvis_EVS: 2.31
• rvis_percentile_EVS: 98.35

Haploinsufficiency Scores

• pHI: 0.122
• hipred: N
• hipred_score: 0.146

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.694

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zswim2

Gene ontology

• Biological process: protein polyubiquitination;apoptotic process;positive regulation of extrinsic apoptotic signaling pathway via death domain receptors
• Molecular function: zinc ion binding;protein self-association;ubiquitin protein ligase activity