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

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

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 (572 variants)
Inborn_genetic_diseases (135 variants)
Neurodevelopmental_disorder_with_dysmorphic_facies_and_distal_skeletal_anomalies (66 variants)
ZMIZ1-related_disorder (17 variants)
not_specified (14 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	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous		1 clinvar	5 clinvar	156 clinvar	20 clinvar	182
missense	3 clinvar	5 clinvar	302 clinvar	55 clinvar	18 clinvar	383
nonsense	6 clinvar	3 clinvar				9
start loss						0
frameshift	11 clinvar	15 clinvar	4 clinvar			30
splice donor/acceptor (+/-2bp)		7 clinvar	2 clinvar			9
Total	20	31	313	211	38

Highest pathogenic variant AF is 0.00000412563

Loading clinvar variants...

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
0.999	0.000634	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

Haploinsufficiency Scores

pHI: 0.400
hipred: Y
hipred_score: 0.825
ghis: 0.679

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

Mouse Genome Informatics

Gene name: Zmiz1
Phenotype: embryo phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system 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); neoplasm; digestive/alimentary phenotype; immune system phenotype; growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); endocrine/exocrine gland phenotype; craniofacial phenotype; cellular phenotype;

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