ZSWIM7

protein-coding

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

Gene summary

Predicted to enable zinc ion binding activity. Involved in double-strand break repair via homologous recombination and protein stabilization. Part of Shu complex. Implicated in ovarian dysgenesis 10 and spermatogenic failure 71. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001042697.2

Inheritance

ClinVar variants

P:4U:27B:2

Top phenotype

Ovarian dysgenesis 10

gnomAD constraint

pLI —, LoF o/e 0.61

Max pathogenic AF

—

Genomic locus

chr17:15,976,560-15,999,717

External References & Databases

Ensembl (ENSG00000214941)

Transcript & Mutation Effects

hg38 • Region Span ~23.2 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

colorectal adenomaLIMITED

Inheritance Pattern: Unknown

Disease ID:MONDO:0005484

Submitter: Ambry Genetics

male infertility with azoospermia or oligozoospermia due to single gene mutationSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0018393

Submitter: King Faisal Specialist Hospital and Research Center

Alhathal et al., 2020 (PMID: 32719396) reported two LOF variants in two independent families with male infertility from a large cohort (n=285 infertile man and case–control fertile man). Gene is scored according to ClinGen classification. Strong with total score of 12. Aggregate-variant analysis (6 points), experimental evidence: Animal model (4 points) (PMID: 30305635) /Protein interaction (1 point) with XRCC2. A known male infertility gene in the humans (PMID: 30042186; PubMed: 16710300) and testicular expression (1 points) (MGI:1916997).

ovarian dysgenesis 10STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0030736

Submitter: Labcorp Genetics (formerly Invitae)

Clinical Genomic Database (CGD)

Ovarian dysgenesis 10AR

Manifestation: Endocrine; Genitourinary; Obstetric

Intervention: Endocrine; Obstetric

Rationale: 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

Refs: 32719396; 33713115; 34402903

Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ZSWIM7 variants in ClinVar

7 Conditions Cataloged

not specifiedTotal: 22

not providedTotal: 7

Inborn genetic diseasesTotal: 4

Spermatogenic failure 71Total: 2

Ovarian dysgenesis 10Total: 2

Non-obstructive azoospermiaTotal: 1

Infertility disorderTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001042697.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar			2
missense		1 clinvar	19 clinvar	2 clinvar		22
nonsense	1 clinvar		1 clinvar			2
start loss						0
frameshift		1 clinvar				1
splice donor/acceptor (+/-2bp)	1 clinvar		5 clinvar			6
Total	2	2	27	2	0	33

Highest pathogenic variant AF is 0.00034763146

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 41 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001042697.2	RefSeq	NP_001036162.1	5	MANE Select
ENST00000399277.6	Ensembl	ENSP00000382218.1	5	MANE Select
NM_001042698.2	RefSeq	NP_001036163.1	5	Standard
ENST00000460252.5	Ensembl	ENSP00000464463.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

double-strand break repair via homologous recombination
protein stabilization

Molecular Function

protein binding
zinc ion binding

Cellular Component

nucleus
Shu complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000399277
Coding exons: 5
Length: 23158
Individuals with no LoFs: 125343
Homozygous LoFs: 0
Heterozygous LoFs: 103
Defined: 125446
p: 0.000411

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.331	67	75.1	0.893	0.00000372	884
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00045	0.00043	rare
Latino/Admixed American	0.00064	0.00064	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.00039	0.00039	rare
Finnish	0.000093	0.000093	rare
European (Non-Finnish)	0.00045	0.00045	rare
South Asian	0.00033	0.00033	rare
Other	0.00050	0.00049	rare

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.315

Gene Damage Prediction

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