SPZ1

spermatogenic leucine zipper 1, the group of Protein phosphatase 1 regulatory subunits

Basic information

Region (hg38): 5:80319624-80321842

Links

ENSG00000164299 ∙ NCBI:84654 ∙ OMIM:618068 ∙ HGNC:30721 ∙ Uniprot:Q9BXG8 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Ciliary dyskinesia, primary, 38	AR	Audiologic/Otolaryngologic; Pulmonary	Among other findings, patients can manifest with early-onset respiratory disease, including upper respiratory infections, and awareness may allow early interventions related to these sequelae	Audiologic/Otolaryngologic; Cardiovascular; Gastrointestinal; Genitourinary; Pulmonary	29727692; 29727693

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SPZ1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPZ1 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				1	1	2
missense			21	2	3	26
nonsense						0
start loss						0
frameshift					1	1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	3	5

Variants in SPZ1

This is a list of pathogenic ClinVar variants found in the SPZ1 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-80320238-C-A		not specified	Uncertain significance (Jun 17, 2024)
5-80320249-A-G		not specified	Uncertain significance (Oct 25, 2022)
5-80320270-C-G		not specified	Uncertain significance (Apr 25, 2022)
5-80320282-C-A		not specified	Uncertain significance (Feb 05, 2024)
5-80320282-C-G		not specified	Uncertain significance (Sep 13, 2022)
5-80320363-C-G		not specified	Uncertain significance (Mar 29, 2022)
5-80320400-A-G		not specified	Uncertain significance (Oct 27, 2023)
5-80320403-A-C		not specified	Uncertain significance (Jun 13, 2023)
5-80320522-A-G		not specified	Uncertain significance (Mar 11, 2024)
5-80320574-A-G		not specified	Uncertain significance (Feb 23, 2023)
5-80320579-A-G		not specified	Uncertain significance (Oct 27, 2023)
5-80320592-A-T		not specified	Uncertain significance (Jul 15, 2021)
5-80320627-A-G		not specified	Uncertain significance (Apr 19, 2023)
5-80320631-A-C		not specified	Uncertain significance (Aug 21, 2023)
5-80320645-A-G		not specified	Uncertain significance (Mar 01, 2024)
5-80320701-A-C		not specified	Uncertain significance (Dec 19, 2022)
5-80320714-A-C		not specified	Uncertain significance (Oct 13, 2023)
5-80320729-T-C		not specified	Uncertain significance (Jan 05, 2022)
5-80320752-A-C		not specified	Uncertain significance (Jun 07, 2024)
5-80320777-A-C		not specified	Uncertain significance (Jul 26, 2022)
5-80320821-C-T			Likely benign (Jul 17, 2018)
5-80320822-G-A		not specified	Uncertain significance (Oct 18, 2021)
5-80320835-C-T		not specified	Uncertain significance (Apr 23, 2024)
5-80320853-G-A		not specified	Likely benign (Dec 14, 2021)
5-80321047-A-G		not specified	Likely benign (Dec 07, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPZ1	protein_coding	protein_coding	ENST00000296739	1	2218

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.717	183	212	0.862	0.00000959	2882
Missense in Polyphen		37	41.01	0.90222		653
Synonymous	-0.273	80	77.0	1.04	0.00000379	742
Loss of Function

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish
East Asian
Finnish
European (Non-Finnish)
Middle Eastern
South Asian
Other

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcription factor that binds to the DNA sequence 5'- CANNTG-3'(E box) and the G-box motif. May play an important role in the regulation of cell proliferation and differentiation during spermatogenesis (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.0722

Intolerance Scores

• loftool: 0.835
• rvis_EVS: 1.57
• rvis_percentile_EVS: 95.71

Haploinsufficiency Scores

• pHI: 0.0397
• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.499

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Spz1

Gene ontology

• Biological process: regulation of transcription, DNA-templated
• Cellular component: nucleus;cytoplasm
• Molecular function: DNA binding;DNA-binding transcription factor activity;protein binding