ZSWIM7

zinc finger SWIM-type containing 7, the group of Zinc fingers SWIM-type

Basic information

Region (hg38): 17:15976560-15999717

Links

ENSG00000214941 ∙ NCBI:125150 ∙ OMIM:614535 ∙ HGNC:26993 ∙ Uniprot:Q19AV6 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• male infertility with azoospermia or oligozoospermia due to single gene mutation (Strong), mode of inheritance: AR
• colorectal adenoma (Limited), mode of inheritance: Unknown
• ovarian dysgenesis 10 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Ovarian dysgenesis 10	AR	Endocrine; Obstetric	The condition involves primary amenorrhea and absent puberty, and medical management (eg, with estrogen replacement therapy) has been described as resulting in onset of puberty	Endocrine; Genitourinary; Obstetric	32719396; 33713115; 34402903

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ZSWIM7 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZSWIM7 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			7	2		9
nonsense						0
start loss						0
frameshift		1				1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			4	7	1	12
Total	0	1	11	9	1

Variants in ZSWIM7

This is a list of pathogenic ClinVar variants found in the ZSWIM7 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-15978064-T-C		not specified	Uncertain significance (Mar 29, 2022)
17-15981101-C-G		not specified	Uncertain significance (Dec 14, 2022)
17-15981113-CAT-C		Non-obstructive azoospermia • Spermatogenic failure 71 • Ovarian dysgenesis 10	Likely pathogenic (Jul 07, 2022)
17-15981116-G-A		not specified	Uncertain significance (Mar 20, 2024)
17-15981122-G-A		not specified	Uncertain significance (Aug 17, 2021)
17-15987265-C-A		Spermatogenic failure 71	Pathogenic (Apr 08, 2022)
17-15987276-C-T		not specified	Likely benign (Aug 23, 2021)
17-15987291-G-A		Infertility disorder	Likely pathogenic (Aug 02, 2022)
17-15987312-T-C		not specified	Uncertain significance (Dec 17, 2021)
17-15987334-C-T		not specified	Uncertain significance (Apr 07, 2022)
17-15999042-C-T			Likely benign (Jul 09, 2018)
17-15999228-G-C			Likely benign (Jun 16, 2018)
17-15999335-T-G			Benign (Jun 14, 2018)
17-15999349-T-G			Likely benign (Nov 16, 2019)
17-15999397-G-A		Mitochondrial complex III deficiency nuclear type 1	Conflicting classifications of pathogenicity (Jul 09, 2018)
17-15999405-T-C		Mitochondrial complex III deficiency nuclear type 1	Uncertain significance (Jun 14, 2016)
17-15999489-G-C		Inborn genetic diseases	Uncertain significance (May 20, 2024)
17-15999502-C-A		not specified • Mitochondrial complex III deficiency nuclear type 1	Benign/Likely benign (Jun 14, 2016)
17-15999509-G-C		not specified • Mitochondrial complex III deficiency nuclear type 1	Conflicting classifications of pathogenicity (Jun 14, 2016)
17-15999521-C-T		Mitochondrial complex III deficiency nuclear type 1 • not specified	Uncertain significance (Apr 06, 2022)
17-15999539-G-A		not specified	Uncertain significance (Jan 16, 2024)
17-15999557-A-G		Inborn genetic diseases	Likely benign (Nov 09, 2023)
17-15999624-G-C		Inborn genetic diseases	Uncertain significance (Nov 30, 2021)
17-15999630-C-A		Inborn genetic diseases	Uncertain significance (Nov 30, 2021)
17-15999645-G-A		Inborn genetic diseases	Likely benign (Feb 08, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZSWIM7	protein_coding	protein_coding	ENST00000399277	5	23158

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000896	0.812	125343	0	103	125446	0.000411

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.331	67	75.1	0.893	0.00000372	884
Missense in Polyphen		14	17.995	0.77801		238
Synonymous	0.673	25	29.7	0.843	0.00000130	268
Loss of Function	1.13	6	9.80	0.612	5.77e-7	105

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00109	0.00107
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.000389	0.000385
Finnish	0.0000928	0.0000927
European (Non-Finnish)	0.000451	0.000449
Middle Eastern	0.000389	0.000385
South Asian	0.000328	0.000327
Other	0.000495	0.000490

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in early stages of the homologous recombination repair (HRR) pathway of double-stranded DNA breaks arising during DNA replication or induced by DNA-damaging agents. {ECO:0000269|PubMed:16710300, ECO:0000269|PubMed:21965664}.

Recessive Scores

• pRec: 0.108

Intolerance Scores

• loftool: 0.614
• rvis_EVS: -0.08
• rvis_percentile_EVS: 47.79

Haploinsufficiency Scores

• pHI: 0.140
• hipred: N
• hipred_score: 0.492
• ghis: 0.604

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.315

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zswim7

Gene ontology

• Biological process: double-strand break repair via homologous recombination;protein stabilization
• Cellular component: nucleus;Shu complex
• Molecular function: protein binding;zinc ion binding