ZMYND15

zinc finger MYND-type containing 15, the group of Zinc fingers MYND-type

Basic information

Region (hg38): 17:4739833-4746119

Links

ENSG00000141497 ∙ NCBI:84225 ∙ OMIM:614312 ∙ HGNC:20997 ∙ Uniprot:Q9H091 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• male infertility with azoospermia or oligozoospermia due to single gene mutation (Supportive), mode of inheritance: AD
• spermatogenic failure 14 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Spermatogenic failure 14	AR	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	Genitourinary	24431330

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ZMYND15 gene.

• Spermatogenic failure 14 (1 variants)
• Non-obstructive azoospermia (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZMYND15 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	2	6
missense			31	3	1	35
nonsense	1					1
start loss						0
frameshift	1					1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2		2
non coding				1		1
Total	2	0	31	8	3

Highest pathogenic variant AF is 0.0000394

Variants in ZMYND15

This is a list of pathogenic ClinVar variants found in the ZMYND15 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-4740606-G-A		not specified	Uncertain significance (Jul 08, 2022)
17-4740666-T-G		not specified	Uncertain significance (Dec 28, 2023)
17-4740693-A-G		not specified	Uncertain significance (Nov 09, 2023)
17-4740754-T-C		not specified	Uncertain significance (Apr 12, 2024)
17-4740892-G-A		not specified	Uncertain significance (Feb 27, 2024)
17-4740896-G-A		ZMYND15-related disorder	Likely benign (Jun 13, 2019)
17-4740915-G-C		not specified	Uncertain significance (Oct 30, 2023)
17-4740923-A-G			Benign (Jul 16, 2018)
17-4740993-C-T		not specified	Uncertain significance (Jan 05, 2022)
17-4741015-A-G		not specified	Uncertain significance (Jan 20, 2023)
17-4741035-G-A		not specified	Uncertain significance (May 07, 2024)
17-4741054-G-A		not specified	Likely benign (Apr 15, 2024)
17-4741128-G-A		not specified	Uncertain significance (May 02, 2024)
17-4741621-C-T		not specified	Uncertain significance (Oct 10, 2023)
17-4741631-T-G		not specified	Uncertain significance (Jul 07, 2022)
17-4741668-G-T		not specified	Uncertain significance (Aug 30, 2021)
17-4741684-G-A		not specified	Uncertain significance (Jun 16, 2024)
17-4741763-T-C			Likely benign (Mar 30, 2018)
17-4741783-G-A		not specified	Likely benign (May 04, 2022)
17-4741813-A-G		not specified	Uncertain significance (Oct 20, 2021)
17-4741915-A-C			Likely benign (Mar 01, 2023)
17-4741986-G-C		not specified	Uncertain significance (May 27, 2022)
17-4741994-T-C		not specified	Uncertain significance (Feb 14, 2023)
17-4742012-C-T		not specified	Uncertain significance (Aug 15, 2023)
17-4742018-C-T		Non-obstructive azoospermia	Pathogenic (Aug 23, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZMYND15	protein_coding	protein_coding	ENST00000573751	13	6093

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.29e-12	0.943	124075	37	1635	125747	0.00667

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.12	369	435	0.849	0.0000249	4775
Missense in Polyphen		118	165.53	0.71287		1893
Synonymous	-0.838	187	173	1.08	0.00000950	1613
Loss of Function	2.12	24	38.1	0.630	0.00000234	372

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0469	0.0469
Ashkenazi Jewish	0.00	0.00
East Asian	0.000981	0.000979
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000389	0.000334
Middle Eastern	0.000981	0.000979
South Asian	0.000131	0.000131
Other	0.00738	0.00719

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a transcriptional repressor through interaction with histone deacetylases (HDACs). May be important for spermiogenesis. {ECO:0000250|UniProtKB:Q8C0R7, ECO:0000303|PubMed:24431330}.
• Disease: DISEASE: Spermatogenic failure 14 (SPGF14) [MIM:615842]: A disorder resulting in the absence (azoospermia) or reduction (oligozoospermia) of sperm in the semen, leading to male infertility. {ECO:0000269|PubMed:24431330}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Intolerance Scores

• loftool: 0.925
• rvis_EVS: -0.95
• rvis_percentile_EVS: 9.27

Haploinsufficiency Scores

• pHI: 0.190
• hipred: N
• hipred_score: 0.384
• ghis: 0.461

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0482

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zmynd15

Gene ontology

• Biological process: spermatid development;negative regulation of transcription, DNA-templated
• Cellular component: nucleus;cytoplasm
• Molecular function: histone deacetylase binding;metal ion binding