ZMYND11

zinc finger MYND-type containing 11, the group of Zinc fingers MYND-type|PHD finger proteins|Bromodomain containing|PWWP domain containing

Basic information

Region (hg38): 10:130088-254637

Links

ENSG00000015171 ∙ NCBI:10771 ∙ OMIM:608668 ∙ HGNC:16966 ∙ Uniprot:Q15326 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• intellectual disability, autosomal dominant 40 (Strong), mode of inheritance: AD
• autosomal dominant non-syndromic intellectual disability (Supportive), mode of inheritance: AD
• intellectual disability, autosomal dominant 30 (Strong), mode of inheritance: AD
• intellectual disability, autosomal dominant 30 (Strong), mode of inheritance: AD
• syndromic complex neurodevelopmental disorder (Definitive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Intellectual developmental disorder, autosomal dominant 30	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; Neurologic	25217958

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ZMYND11 gene.

• not provided (21 variants)
• Intellectual disability, autosomal dominant 30 (14 variants)
• Inborn genetic diseases (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZMYND11 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			1	34	3	38
missense	2	10	80	8	8	108
nonsense	8	5				13
start loss						0
frameshift	18	5	1			24
inframe indel			3		1	4
splice donor/acceptor (+/-2bp)	1	2				3
splice region		1	6	5	1	13
non coding			4	29	15	48
Total	29	22	89	71	27

Variants in ZMYND11

This is a list of pathogenic ClinVar variants found in the ZMYND11 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-134787-G-A			Uncertain significance (Jan 19, 2024)
10-134900-C-A		Intellectual disability, autosomal dominant 30	Uncertain significance (-)
10-180016-G-A		Intellectual disability, autosomal dominant 30	Likely pathogenic (Mar 25, 2021)
10-180020-G-A			Likely benign (Nov 20, 2023)
10-180032-G-C		Inborn genetic diseases	Uncertain significance (Feb 23, 2023)
10-180032-G-T			Uncertain significance (Dec 05, 2023)
10-180034-C-T		Intellectual disability, autosomal dominant 30	Pathogenic (Dec 31, 2022)
10-180040-G-A			Uncertain significance (Aug 03, 2017)
10-180042-G-A			Likely benign (Jan 25, 2024)
10-180049-A-G		Intellectual disability, autosomal dominant 30	Uncertain significance (Dec 13, 2022)
10-180058-C-T			Pathogenic (Apr 30, 2018)
10-180076-A-G		Intellectual disability, autosomal dominant 30	Uncertain significance (May 01, 2023)
10-180088-C-T		Intellectual disability, autosomal dominant 30	Pathogenic/Likely pathogenic (May 24, 2023)
10-180094-C-T		Intellectual disability, autosomal dominant 30	Pathogenic (Apr 13, 2021)
10-180113-T-C			Uncertain significance (Sep 10, 2020)
10-180118-C-T		See cases	Uncertain significance (Oct 20, 2022)
10-180146-C-T			Likely benign (Jan 15, 2024)
10-180148-A-G			Benign (Jan 22, 2024)
10-205651-T-A		Paragangliomas 5	Uncertain significance (Jan 20, 2016)
10-209352-T-TTGCCTGACTGATCACAACATGCGTCCATGCTTTCCTTATATGTTGACAAGCACTCGTGTAATTTCTAAATGTTCTCTGGTGTCATTTCCTAAGTTTTAGGTAAAAGTATTACAAAATATGTTTGTAGTTCTAAGGTCCTATGGTTGGAGATTATAAAATTCTAAATGTAGAATCTGTAGAGTAGAAGTTAGTGGTAATTGCTCCCTCTGGAGGCTAAAACTAAATGGGATGTTTGACTACAGTCTCTTAAGTGATTTATATTCGCTGATTTGGGACTATTTTGAACATATCTTGGTCTAATCATTACAGAAGAGAATTTGAGTTTAAAATAGCATGATAATTGGAAGAGTTGCGTATTGAAGACTTTTCCTTTCTTTTCTGTTTATCGTGTTCGTTCTTTATCTTGTTCTTTATCTCAACAGGACTCTCATAAATACAAGTCATAATGAAAGAAATTACCACCATTTTCTTATTTTCATTCATTTTTAGTTTTCAGTACTGAAAGATTTTTAAATTTGTTTTTCCTCTGTGTTCAGGTATATGTCTCGAGTCCACGGTATGCACCCTAAAGAGACCACCCGTCAGCTGAGCTTAGCTGTGAAAGATGGTCTTATTGTCGAAACTCTAACAGTGGGCTGCAAAGGTTCAAAAGCTGGTATTGAACAAGAAGGATATTGGTTGCCAGGAGATGAGATTGTAAGTACATTTTATTTGATAAACATAGAGATGTGAACTTTTAGCTTTTAAACATTATTTAGATACAACCTATAGAAAATCATTTTCAGAAGTTTAATATTTCATTTTAACATTTGTATCAACATTAAGGCTCTACATTGGTAGTATGGATACTTTCCTTACTAATTATTTAGGAGATGACTCACTTTTACAAAGATCCTGCTTCTCTATATATTACCTTGAATCTAAAAAAGAAAGCAAACCAAAGCTCTTTTGATGTACCCACACTTCATGGCATTCCTAAGTGTTTTCGTCAATAAATATTAGCAAAAAATGTTTCCATGCCAGATAATGTTGATGCCATCTAGACAGATAGAAGGGGATGAACCGTCTTCCTAGGGAAACAGCCTCAGTTCAGGTAGGATGGTATCACAGCCCAAAGGCAGGCTTCAGTAGGAATTTTGTGGCAGAGTACAAAGGTTCCAAACGTTAAGTTCTCCTGGCCAGTGCCTACGTTGACTAATGACAATTGCAAGTTTTGTGTACTGGAACAGAAATCAAATAGGAAAGACAGAACATTAATTCTCTTTACGTTTTTACCTAGTTCTCACTTTGACTCCTCTTTTAAATGTTGATATTTTAATCTGCTTCTCTTTCCTTTCATTATGTACCTTTAAACTCAGAGGCACATATCGAAGTACATTTTTTTCTTACGTAAAGATTGATTTCATGTGTAATATTTCTATCTTCCTACCTTATTTTATTTTGCTGTTTCTAATACCTTGATTTAAAATGTGTTAATTTTTACAAGGGAACATCATTTAAGATGATAGGTTTCAAATGTAACAGATGTGGCCAGGTGTGGTGGCTCATGCCTGTAGTCCTAGCACTTTGGAAGGCTAAAGCAGGAGGATCACTTGAGCCCAGGAGTTCAACACTAGCCTGGGCAACATAGCCCCCATCTCTACAAAAAAAAATAAAATACACAACCCCATCTCTACAAAAAAATAAAAAATTAGCTGGGTGTGGTGGCACATGCCTGTAGTACCAGATACCCAGGAGGCTGAGGTAGGAGGATCACTTGAGCCCAGGAGTTTAGGGCTGCAATGAGCTATGGTCATGCCGCTGCTGTACTGTAGCCTGGGCGACAGAGCAAGACCCTGTCTCCTAAAAAGAAAAAAAAAAATCTATCTATAGATATCTTTTTCTTAAAAAGAAAAAAAAAATCTATCTATAGATATAGATAGACATATCCCTTTCAAAAATCTATCTCTTTCTATAGATTGAGTTTGTGAAAGGGATAGATTTAGTAATTGCATACTTTGAGAGTGTTTTATCATAAATTCTCTAAAATCTAAAATTATAAAAATGACATAGAATCTTATAATTGGTTCTTTGTGGAAAAATTTTCCAAAAAGTTTGAGTTTATTTTCTTTTCTGGCTCTACAGCAGATGAGCCAGCAAACATACTAACCTGTGAAGCCTGAGAGCAGTAAACTAACTAGCAAGTGCCTGTGGGGAGGTGGTTTATAGCAACAGCTGTGATAAGGTATAAACTTAGAAAAGCTGTTCACTTCTTTAACTTTGTTTTTGTCAATTTAATCTGCACCTTCAAAGCTTCAGGAAAGAACATTCACATTTTCCAGCAACAGAAAACATGGAAGAAAAAATCTTTACTTTCACTGGTGTAATTTCATTTGTGCACTGGAAGTATTCTTGAAAAGTTAAGTGGAAATCTTTATATAAGAAGAATTTTTCTATTGAGTTGCCTTACAGAAAAGTAAAGCTTTGCTGCCAGTGAAGAAACTTAGGGTGCCAAGACATAATAAAAGTAATGTCAAGTGGTATCAGTCTATTGCCTCAGGTATTTAAAGGAGGGCCATTAATTGTTGATACCTTATTATATACTCAGAATAATCCAGATAATGTAAAATTTCTAATCTTAAAACACTTAGGAATTTATAGATAGTATAGAAGACTATAGTGATAATATCCAAGATTTGTATAGTAATTAACTAACAGTAAGTGCAACTTAATCTATAGGATTTTGGTTTGTGGATCATGTGTACATTTTTTCATAAAAGCGATTTTATTTCTCTTTACTGTTTAGATTGGTACTTTCCTATATGCTTTCTTCCTCCTCAAGTTGAAGTTTTTTTGTTTAGTTTAATTCAATAAGTCGTTAATGAGCACATTATATTTTTACCACTATATTAGGTCCTATGTTCTAATTTTTATTTTTATATGTTGTTCTTGCATATATTTATAGAATCATCCTTTTTTCTTCTGTCTAGATGAAATATTATATGTAAACCAAACATATAGTATACAGGTTTAATTCTGATTGGTTCTTTCTTGCAAACATTTTTATTCTAAAATGGCTGTATAATATAAGCACAAGTGAATATATCAAAATTGTGCCTGGTGTATAAAATATGTAAATATTTAAAATTCAGAGGTAATGTAGTTTATTAGAAAGAAGTAAGATCTCGTATGTCACAAATAAACAGGGGTTTCAGATCCAATTCAAGCCTTTATTTAGTTATGCAACCTTGAGGAAATTTCTTAGCCTCTGATCCTCAGCCCTCAGCTGTCGTATGGGCATATTAATATCTATTTCATTTGATTGTTTGAAAGATTAAATGAGATTATCTACATAAAGTGTATAACCAGGTACTCAAAGCAAGTTTTTGACCAATGAATAAATATGCTTACAACAAAAAACGCCTGTATATAATATAGTAAAAGCACATTAGTTTCTTACTAATTATACAAGCAAAAATTCTACTCAGGGTCTTTTTACTTTTCAACCTGTATTCTCAAACACAAGACTTGTAAAGAGGTTTTCCATTAGAACACTGGATCTTTATTTAAAGTGTAACTCTAAAATAATGAGACAAATTATATGTGTATTTTGTTACCTTGGCTGGGGTCCCACCTGGCTACTCAGCGACTGTCCATGTGCCACAATTTTCATGCCCTGATAACACTCTAGGAGGAGGACATATAATTGTTTCCCACTAGGCACAGCACATGCATCTCGTACTGACCAGCTTTGTGTACTTTTTTTAATGTATGGCCAGTGCGTGGAGGTTGTTGCATATGGGGGTGCCAGATGTGAACTGTACAATTTAGGAAGCCCCATCCACATCACAGACATTGTATATTTGCCTATTTATTCAAAAGTCACCAGTGCATTTATTCTAATAAATGAACATACAACAACAAGAGTGTCTTATGGAAGGGCCACCTTTTCTAGTTTGCACATGGTGTTCTGTGGGCTAATGATTGTCCTACATGCCAGCATTTGAGTCTGGGGCCCATGCTTTATAGTTTTACCACCTTATATATAGGATGAATCACTTTGATGTCTCTAAAAACTTGACTTTTTAAACTGAAAGATGTA		Intellectual disability, autosomal dominant 30	Uncertain significance (Jul 01, 2021)
10-209870-G-A			Benign (Dec 25, 2023)
10-209870-G-T			Likely benign (Dec 09, 2023)
10-209900-G-A		See cases	Uncertain significance (Dec 21, 2021)
10-209900-G-C		Intellectual disability, autosomal dominant 30	Uncertain significance (Feb 23, 2023)
10-209902-G-A			Uncertain significance (Nov 08, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZMYND11	protein_coding	protein_coding	ENST00000397962	14	120173

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.00000344	125733	0	6	125739	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.71	158	355	0.446	0.0000205	4043
Missense in Polyphen		36	163	0.22085		1863
Synonymous	-0.411	122	116	1.05	0.00000657	1014
Loss of Function	5.68	1	39.6	0.0253	0.00000230	432

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000353	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000171	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Chromatin reader that specifically recognizes and binds histone H3.3 trimethylated at 'Lys-36' (H3.3K36me3) and regulates RNA polymerase II elongation. Does not bind other histone H3 subtypes (H3.1 or H3.2) (By similarity). Colocalizes with highly expressed genes and functions as a transcription corepressor by modulating RNA polymerase II at the elongation stage. Binds non- specifically to dsDNA (PubMed:24675531). Acts as a tumor- suppressor by repressing a transcriptional program essential for tumor cell growth. {ECO:0000250|UniProtKB:Q8R5C8, ECO:0000269|PubMed:10734313, ECO:0000269|PubMed:16565076, ECO:0000269|PubMed:24675531}.
• Disease: DISEASE: Note=A chromosomal aberration involving ZMYND11 is a cause of acute poorly differentiated myeloid leukemia. Translocation (10;17)(p15;q21) with MBTD1. {ECO:0000269|PubMed:23915195}.; DISEASE: Mental retardation, autosomal dominant 30 (MRD30) [MIM:616083]: A disorder characterized by significantly below average general intellectual functioning associated with impairments in adaptive behavior and manifested during the developmental period. MRD30 patients manifest mild intellectual disability and subtle facial dysmorphisms, including hypertelorism, ptosis, and a wide mouth. {ECO:0000269|PubMed:25217958}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Regulation of toll-like receptor signaling pathway (Consensus)

Recessive Scores

• pRec: 0.120

Intolerance Scores

• loftool: 0.122
• rvis_EVS: -0.49
• rvis_percentile_EVS: 22.09

Haploinsufficiency Scores

• pHI: 0.183
• hipred: Y
• hipred_score: 0.831
• ghis: 0.691

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.881

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zmynd11
• Phenotype: craniofacial phenotype; muscle phenotype; endocrine/exocrine gland phenotype; growth/size/body region phenotype; embryo phenotype; skeleton phenotype; immune system phenotype; vision/eye phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); digestive/alimentary phenotype; reproductive system 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); respiratory system phenotype; liver/biliary system phenotype

Gene ontology

• Biological process: chromatin organization;cell cycle;cell population proliferation;viral process;regulation of transcription elongation from RNA polymerase II promoter;negative regulation of I-kappaB kinase/NF-kappaB signaling;negative regulation of JNK cascade;defense response to virus;negative regulation of nucleic acid-templated transcription;negative regulation of extrinsic apoptotic signaling pathway
• Cellular component: nucleus;nucleoplasm;chromosome
• Molecular function: double-stranded DNA binding;transcription corepressor activity;protein binding;zinc ion binding;methylated histone binding