ZSWIM3

zinc finger SWIM-type containing 3, the group of Zinc fingers SWIM-type

Basic information

Region (hg38): 20:45857613-45879122

Previous symbols: [ "C20orf164" ]

Links

ENSG00000132801 ∙ NCBI:140831 ∙ ∙ HGNC:16157 ∙ Uniprot:Q96MP5 ∙ 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 ZSWIM3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZSWIM3 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			30	2		32
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	30	2	0

Variants in ZSWIM3

This is a list of pathogenic ClinVar variants found in the ZSWIM3 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-45857899-G-A		not specified	Uncertain significance (Mar 06, 2023)
20-45876764-G-A		not specified	Uncertain significance (Jun 03, 2024)
20-45876769-C-T		not specified	Uncertain significance (Aug 04, 2023)
20-45876783-G-A		not specified	Uncertain significance (Jan 12, 2024)
20-45876798-G-T		not specified	Uncertain significance (Jan 19, 2024)
20-45876818-G-A		not specified	Likely benign (Oct 25, 2022)
20-45876875-A-T		not specified	Uncertain significance (Feb 27, 2023)
20-45876878-T-C		not specified	Uncertain significance (Dec 05, 2022)
20-45876883-A-C		not specified	Uncertain significance (Nov 17, 2023)
20-45876977-C-G		not specified	Uncertain significance (Jun 17, 2024)
20-45877123-A-G		not specified	Uncertain significance (Oct 25, 2022)
20-45877163-G-A		not specified	Uncertain significance (Jun 09, 2022)
20-45877342-G-C		not specified	Uncertain significance (Apr 07, 2022)
20-45877381-G-A		not specified	Uncertain significance (Jan 16, 2024)
20-45877448-T-A		not specified	Uncertain significance (Oct 26, 2022)
20-45877493-G-T		not specified	Uncertain significance (Mar 18, 2024)
20-45877517-G-A		not specified	Uncertain significance (Oct 16, 2023)
20-45877564-C-T		not specified	Uncertain significance (Dec 07, 2021)
20-45877592-C-T		not specified	Uncertain significance (Feb 06, 2024)
20-45877597-C-G		not specified	Uncertain significance (Jun 29, 2023)
20-45877604-A-G		not specified	Uncertain significance (Sep 01, 2021)
20-45877873-C-T		not specified	Uncertain significance (Jul 12, 2023)
20-45877900-A-C		not specified	Uncertain significance (Nov 03, 2023)
20-45877984-G-A		not specified	Uncertain significance (May 26, 2024)
20-45878053-C-T		not specified	Uncertain significance (Aug 12, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZSWIM3	protein_coding	protein_coding	ENST00000255152	2	21506

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000552	0.994	125708	0	40	125748	0.000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.64	301	392	0.767	0.0000220	4597
Missense in Polyphen		79	138.5	0.57038		1701
Synonymous	0.143	155	157	0.985	0.00000860	1366
Loss of Function	2.44	11	23.9	0.461	0.00000136	254

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000424	0.000423
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000647	0.000647
European (Non-Finnish)	0.0000887	0.0000879
Middle Eastern	0.00	0.00
South Asian	0.000131	0.000131
Other	0.000489	0.000489

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.524
• rvis_EVS: -0.11
• rvis_percentile_EVS: 45.49

Haploinsufficiency Scores

• pHI: 0.0878
• hipred: N
• hipred_score: 0.242
• ghis: 0.500

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.522

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zswim3

Gene ontology

• Molecular function: zinc ion binding