ZPR1

ZPR1 zinc finger, the group of Zinc fingers

Basic information

Region (hg38): 11:116773798-116788039

Previous symbols: [ "ZNF259" ]

Links

ENSG00000109917 ∙ NCBI:8882 ∙ OMIM:603901 ∙ HGNC:13051 ∙ Uniprot:O75312 ∙ 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
Growth restriction, hypoplastic kidneys, alopecia, and distinctive facies	AR	Audiologic/Otolaryngologic; Renal	Among other findings, the condition can involve hearing loss, and early recognition and treatment of hearing impairment may improve outcomes, including speech and language development; As the condition can include renal anomalies, with morbidity and mortality reported to involve uremia, awareness may allow early interventions related to these manifestations	Audiologic/Otolaryngologic; Craniofacial; Dental; Genitourinary; Hematologic; Musculoskeletal; Neurologic; Renal	29851065

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ZPR1 gene.

• Inborn genetic diseases (18 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZPR1 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			18	1	1	20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	1	1

Variants in ZPR1

This is a list of pathogenic ClinVar variants found in the ZPR1 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-116778929-C-T		not specified	Uncertain significance (Jan 19, 2022)
11-116778930-G-A		not specified	Uncertain significance (Mar 06, 2023)
11-116778938-G-C		not specified	Uncertain significance (Dec 03, 2021)
11-116779016-C-G		not specified	Uncertain significance (Mar 20, 2023)
11-116779044-C-G		not specified	Uncertain significance (Jun 09, 2022)
11-116779049-G-A			Benign (May 18, 2018)
11-116779782-C-A		not specified	Uncertain significance (Aug 12, 2022)
11-116782176-A-T			Likely benign (Aug 01, 2023)
11-116782927-G-A		not specified	Uncertain significance (Sep 22, 2023)
11-116782948-C-T		not specified	Uncertain significance (Nov 18, 2023)
11-116783549-A-G		not specified	Uncertain significance (May 22, 2023)
11-116783581-C-G		not specified	Uncertain significance (Aug 16, 2021)
11-116784389-G-A		not specified	Uncertain significance (Sep 28, 2021)
11-116784413-T-C		not specified	Uncertain significance (Dec 21, 2023)
11-116784902-T-A		not specified	Uncertain significance (Jul 06, 2021)
11-116785542-C-T		not specified	Likely benign (Apr 25, 2022)
11-116785572-G-A		not specified	Uncertain significance (Aug 12, 2021)
11-116785632-A-G		Growth restriction, hypoplastic kidneys, alopecia, and distinctive facies	Pathogenic (May 10, 2021)
11-116785849-C-T		not specified	Uncertain significance (Aug 17, 2022)
11-116785870-C-G		not specified	Uncertain significance (Sep 14, 2022)
11-116787500-C-A		not specified	Uncertain significance (Dec 03, 2021)
11-116787579-G-A		not specified	Uncertain significance (Apr 25, 2022)
11-116787833-T-G		not specified	Uncertain significance (Feb 15, 2023)
11-116787876-C-T		not specified	Uncertain significance (Feb 02, 2022)
11-116787930-C-T		not specified	Uncertain significance (Jul 13, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZPR1	protein_coding	protein_coding	ENST00000227322	14	10331

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.95e-9	0.912	125701	0	47	125748	0.000187

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.726	216	248	0.870	0.0000126	3004
Missense in Polyphen		73	89.037	0.81988		1088
Synonymous	0.763	83	92.3	0.899	0.00000463	863
Loss of Function	1.81	17	27.2	0.625	0.00000155	296

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000206	0.000206
Ashkenazi Jewish	0.00	0.00
East Asian	0.000598	0.000598
Finnish	0.0000464	0.0000462
European (Non-Finnish)	0.000203	0.000202
Middle Eastern	0.000598	0.000598
South Asian	0.000163	0.000163
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a signaling molecule that communicates proliferative growth signals from the cytoplasm to the nucleus. Plays a role for the localization and accumulation of the survival motor neuron protein SMN1 in sub-nuclear bodies, including gems and Cajal bodies. Induces neuron differentiation and stimulates axonal growth and formation of growth cone in spinal cord motor neurons. Plays a role in the splicing of cellular pre-mRNAs. May be involved in H(2)O(2)-induced neuronal cell death. {ECO:0000269|PubMed:11283611, ECO:0000269|PubMed:17068332, ECO:0000269|PubMed:22422766}.
• Pathway: EGFR1 (Consensus)

Recessive Scores

• pRec: 0.119

Intolerance Scores

• rvis_EVS: 0.24
• rvis_percentile_EVS: 69.37

Haploinsufficiency Scores

• pHI: 0.340
• hipred: N
• hipred_score: 0.488
• ghis: 0.518

Essentials

• essential_gene_gene_trap: E

Mouse Genome Informatics

• Gene name: Zpr1
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); embryo phenotype; cellular phenotype

Gene ontology

• Biological process: microtubule cytoskeleton organization;inner cell mass cell proliferation;trophectodermal cell proliferation;mRNA processing;signal transduction;cell population proliferation;RNA splicing;positive regulation of gene expression;spinal cord development;Cajal body organization;regulation of myelination;positive regulation of RNA splicing;DNA endoreduplication;positive regulation of protein import into nucleus;positive regulation of growth;axon development;cellular response to epidermal growth factor stimulus;positive regulation of transcription involved in G1/S transition of mitotic cell cycle;apoptotic process involved in development;pre-mRNA catabolic process;negative regulation of motor neuron apoptotic process
• Cellular component: nucleus;nucleoplasm;nucleolus;cytoplasm;Cajal body;axon;growth cone;SMN complex;neuronal cell body;perikaryon;perinuclear region of cytoplasm;Gemini of coiled bodies
• Molecular function: protein binding;zinc ion binding;receptor tyrosine kinase binding;translation initiation factor binding