ZMIZ1

zinc finger MIZ-type containing 1, the group of Zinc fingers MIZ-type

Basic information

Region (hg38): 10:79068966-79316519

Previous symbols: [ "RAI17" ]

Links

ENSG00000108175 ∙ NCBI:57178 ∙ OMIM:607159 ∙ HGNC:16493 ∙ Uniprot:Q9ULJ6 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• neurodevelopmental disorder with dysmorphic facies and distal skeletal anomalies (Moderate), mode of inheritance: AD
• complex neurodevelopmental disorder (Definitive), mode of inheritance: AD
• neurodevelopmental disorder with dysmorphic facies and distal skeletal anomalies (Strong), mode of inheritance: AD
• syndromic intellectual disability (Supportive), mode of inheritance: AD
• neurodevelopmental disorder with dysmorphic facies and distal skeletal anomalies (Strong), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Neurodevelopmental disorder with dysmorphic facies and distal skeletal anomalies	AD	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Craniofacial; Musculoskeletal; Neurologic; Ophthalmologic	30639322

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ZMIZ1 gene.

• not_provided (632 variants)
• Inborn_genetic_diseases (153 variants)
• Neurodevelopmental_disorder_with_dysmorphic_facies_and_distal_skeletal_anomalies (74 variants)
• ZMIZ1-related_disorder (17 variants)
• not_specified (15 variants)
• Syndromic_neurodevelopmental_disorder (13 variants)
• See_cases (3 variants)
• Neurodevelopmental_abnormality (2 variants)
• Neurodevelopmental_disorder (1 variants)
• Autism_spectrum_disorder (1 variants)
• Intellectual_disability (1 variants)
• Developmental_disorder (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZMIZ1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000020338.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous		1	8	170	18	197
missense	3	5	332	62	19	421
nonsense	6	4				10
start loss						0
frameshift	10	18	4			32
splice donor/acceptor (+/-2bp)		8	7			15
Total	19	36	351	232	37

Highest pathogenic variant AF is 0.000004125634

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZMIZ1	protein_coding	protein_coding	ENST00000334512	21	247485

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
		125733	0	13	125746	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.39	447	699	0.639	0.0000444	7017
Missense in Polyphen		129	265.38	0.4861		2544
Synonymous	-0.684	318	303	1.05	0.0000224	2138
Loss of Function	5.79	7	52.1	0.134	0.00000265	521

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000236	0.000235
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000178	0.0000176
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000980	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as transcriptional coactivator. Increases ligand- dependent transcriptional activity of AR and promotes AR sumoylation. The stimulation of AR activity is dependent upon sumoylation (PubMed:14609956, PubMed:26522984). Involved in transcriptional activation of a subset of NOTCH1 target genes including MYC. Involved in thymocyte and T cell development (By similarity). {ECO:0000250|UniProtKB:Q6P1E1, ECO:0000269|PubMed:14609956, ECO:0000269|PubMed:26522984}.
• Pathway: Androgen receptor signaling pathway;AndrogenReceptor;Coregulation of Androgen receptor activity (Consensus)

Recessive Scores

• pRec: 0.123

Intolerance Scores

• loftool: 0.154
• rvis_EVS: -2.04
• rvis_percentile_EVS: 1.66

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: K
• gene_indispensability_pred: E
• gene_indispensability_score: 0.956

Gene Damage Prediction

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

Gene ontology

• Biological process: vasculogenesis;in utero embryonic development;heart morphogenesis;vitellogenesis;cell aging;positive regulation of T cell differentiation;positive regulation of Notch signaling pathway;positive regulation of transcription by RNA polymerase II;positive regulation of fibroblast proliferation;developmental growth;artery morphogenesis
• Cellular component: nucleoplasm;cytoplasm;nuclear speck;intracellular membrane-bounded organelle
• Molecular function: zinc ion binding