ZMIZ1

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

Basic information

Region (hg38): 10:79068965-79316519

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

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 (320 variants)
• Inborn genetic diseases (59 variants)
• Neurodevelopmental disorder with dysmorphic facies and distal skeletal anomalies (32 variants)
• ZMIZ1-related condition (8 variants)
• not specified (6 variants)
• Intellectual disability (5 variants)
• Syndromic neurodevelopmental disorder (5 variants)
• See cases (2 variants)
• Neurodevelopmental abnormality (1 variants)
• Developmental disorder (1 variants)
• Neurodevelopmental disorder (1 variants)
• Autism spectrum 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.

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			3	84	23	110
missense	2	3	154	20	4	183
nonsense	3	2				5
start loss						0
frameshift	4	6	4			14
inframe indel		1	7	2		10
splice donor/acceptor (+/-2bp)		5	1			6
splice region			8	9	5	22
non coding			1	33	15	49
Total	9	17	170	139	42

Variants in ZMIZ1

This is a list of pathogenic ClinVar variants found in the ZMIZ1 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-79184473-T-G			Benign (Feb 18, 2020)
10-79201626-G-A			Benign (Mar 01, 2023)
10-79201654-A-T		Inborn genetic diseases	Uncertain significance (Apr 06, 2023)
10-79201667-A-G		Inborn genetic diseases	Uncertain significance (Nov 08, 2021)
10-79201669-G-A			Uncertain significance (Jun 01, 2022)
10-79201683-C-T			Benign (Dec 04, 2023)
10-79201703-G-C			Likely benign (Dec 01, 2023)
10-79208350-T-G			Likely benign (Dec 24, 2022)
10-79208354-A-G			Uncertain significance (Dec 08, 2022)
10-79208360-C-T			Likely benign (Dec 11, 2023)
10-79208368-C-T			Likely benign (Jan 01, 2024)
10-79208378-C-G			Uncertain significance (Mar 14, 2023)
10-79208380-G-T			Likely benign (May 25, 2022)
10-79208381-C-T			Likely benign (Jun 15, 2023)
10-79208392-C-T			Likely benign (Aug 23, 2022)
10-79208393-G-A		Neurodevelopmental disorder with dysmorphic facies and distal skeletal anomalies	Uncertain significance (Feb 02, 2022)
10-79208410-C-T			Benign (Jan 25, 2024)
10-79208412-A-G			Uncertain significance (Jun 19, 2022)
10-79208415-G-A		Inborn genetic diseases	Likely benign (Nov 01, 2023)
10-79208427-AGAGCCT-A			Uncertain significance (Mar 24, 2023)
10-79208430-G-A			Uncertain significance (May 24, 2022)
10-79208434-G-A			Likely benign (Oct 17, 2023)
10-79208444-T-G		Inborn genetic diseases	Uncertain significance (Dec 27, 2023)
10-79208448-C-T		Inborn genetic diseases • See cases	Uncertain significance (Feb 24, 2023)
10-79208452-G-A			Uncertain significance (Dec 09, 2023)

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