ZMYM3

zinc finger MYM-type containing 3, the group of Zinc fingers MYM-type

Basic information

Region (hg38): X:71239623-71255146

Previous symbols: [ "ZNF261" ]

Links

ENSG00000147130 ∙ NCBI:9203 ∙ OMIM:300061 ∙ HGNC:13054 ∙ Uniprot:Q14202 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• intellectual disability (Limited), mode of inheritance: XL
• syndromic intellectual disability (No Known Disease Relationship), mode of inheritance: XL

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Intellectual developmental disorder, X-linked 112	XL	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	24721225; 36586412

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ZMYM3 gene.

• not provided (47 variants)
• Inborn genetic diseases (20 variants)
• ZMYM3-related condition (5 variants)
• not specified (3 variants)
• Intellectual disability (1 variants)
• Intellectual developmental disorder, X-linked 112 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZMYM3 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			4	10	3	17
missense			45	1	2	48
nonsense						0
start loss						0
frameshift			2			2
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region				2	1	3
non coding						0
Total	0	0	52	11	5

Variants in ZMYM3

This is a list of pathogenic ClinVar variants found in the ZMYM3 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-71240948-G-A		ZMYM3-related disorder	Likely benign (Feb 22, 2019)
X-71240964-G-A			Conflicting classifications of pathogenicity (Dec 31, 2019)
X-71240973-C-T		not specified	Likely benign (Dec 03, 2015)
X-71241080-C-T		Inborn genetic diseases	Uncertain significance (Jan 24, 2024)
X-71241084-G-A			Benign (Dec 31, 2019)
X-71241095-G-A			Uncertain significance (Aug 31, 2022)
X-71241267-G-A		not specified • Intellectual developmental disorder, X-linked 112	Conflicting classifications of pathogenicity (Jul 30, 2015)
X-71241303-T-C		Inborn genetic diseases	Uncertain significance (Mar 02, 2023)
X-71241334-A-G			Likely benign (Feb 08, 2018)
X-71241338-C-T		Inborn genetic diseases	Uncertain significance (Nov 15, 2023)
X-71241348-T-C		ZMYM3-related disorder	Benign (Apr 11, 2019)
X-71241353-G-T		ZMYM3-related disorder	Likely benign (Feb 05, 2020)
X-71242172-C-T		Intellectual disability	Uncertain significance (Sep 10, 2020)
X-71242187-C-T		Inborn genetic diseases	Uncertain significance (Feb 27, 2024)
X-71242198-A-G			Uncertain significance (Nov 01, 2018)
X-71242232-C-T		Inborn genetic diseases	Uncertain significance (Dec 15, 2021)
X-71242260-G-A			Uncertain significance (Nov 09, 2022)
X-71242420-C-T			Uncertain significance (Jan 08, 2014)
X-71243010-G-A		ZMYM3-related disorder	Likely benign (Sep 01, 2022)
X-71243066-G-A			Uncertain significance (May 01, 2019)
X-71243890-C-T			Uncertain significance (May 02, 2019)
X-71243913-G-C			Likely benign (Mar 01, 2023)
X-71243982-T-C			Uncertain significance (May 12, 2023)
X-71244447-G-A		ZMYM3-related disorder	Likely benign (Oct 30, 2020)
X-71244460-C-T			Uncertain significance (Mar 24, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZMYM3	protein_coding	protein_coding	ENST00000353904	24	15523

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	5.38e-7	122830	1	0	122831	0.00000407

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	4.31	261	543	0.480	0.0000453	8908
Missense in Polyphen		87	248.42	0.35021		3916
Synonymous	-0.297	210	205	1.03	0.0000160	2722
Loss of Function	6.05	1	44.6	0.0224	0.00000343	775

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000124	0.00000901
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in the regulation of cell morphology and cytoskeletal organization. {ECO:0000269|PubMed:21834987}.

Recessive Scores

• pRec: 0.142

Intolerance Scores

• loftool: 0.0320
• rvis_EVS: -1.18
• rvis_percentile_EVS: 5.97

Haploinsufficiency Scores

• pHI: 0.610
• hipred: Y
• hipred_score: 0.825
• ghis: 0.623

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.892

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zmym3

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;cytoskeleton organization;multicellular organism development;regulation of cell morphogenesis
• Cellular component: nucleus;nucleoplasm
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;zinc ion binding