ZMYM5

zinc finger MYM-type containing 5, the group of Zinc fingers MYM-type

Basic information

Region (hg38): 13:19823482-19863649

Previous symbols: [ "ZNF237" ]

Links

ENSG00000132950 ∙ NCBI:9205 ∙ OMIM:616443 ∙ HGNC:13029 ∙ Uniprot:Q9UJ78 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• multiple congenital anomalies/dysmorphic syndrome (Limited), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ZMYM5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZMYM5 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						0
missense			21	1		22
nonsense					1	1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	1	1

Variants in ZMYM5

This is a list of pathogenic ClinVar variants found in the ZMYM5 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-19835614-C-T		not specified	Uncertain significance (Sep 16, 2021)
13-19835644-T-C		not specified	Uncertain significance (Jul 20, 2021)
13-19835661-A-T		not specified	Uncertain significance (Jul 26, 2022)
13-19835664-T-A		not specified	Uncertain significance (Feb 06, 2024)
13-19835685-C-T		not specified	Uncertain significance (Mar 15, 2024)
13-19837694-T-G		not specified	Uncertain significance (Dec 18, 2023)
13-19837802-C-A		not specified	Uncertain significance (Apr 26, 2023)
13-19837810-G-A		not specified	Uncertain significance (May 12, 2024)
13-19837811-T-C		not specified	Uncertain significance (Feb 23, 2023)
13-19837819-T-A		not specified	Uncertain significance (Nov 30, 2021)
13-19838769-C-A		not specified	Uncertain significance (Jun 16, 2023)
13-19838811-C-T		not specified	Uncertain significance (Oct 20, 2021)
13-19838862-G-T		not specified	Uncertain significance (Feb 23, 2023)
13-19838948-A-C		not specified	Uncertain significance (Aug 10, 2021)
13-19851730-T-C		not specified	Uncertain significance (May 24, 2024)
13-19851738-T-C		not specified	Uncertain significance (Jun 05, 2023)
13-19851839-A-C		not specified	Uncertain significance (Mar 01, 2024)
13-19851877-A-C		not specified	Uncertain significance (May 05, 2023)
13-19851877-A-G		not specified	Likely benign (Feb 22, 2023)
13-19852002-A-T		not specified	Uncertain significance (Sep 15, 2021)
13-19852005-T-C		not specified	Uncertain significance (Oct 05, 2023)
13-19852035-G-C			Benign (Dec 31, 2019)
13-19852093-C-T		not specified	Uncertain significance (Aug 19, 2023)
13-19852111-T-C		not specified	Uncertain significance (Mar 08, 2024)
13-19852139-C-G		not specified	Uncertain significance (Aug 02, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZMYM5	protein_coding	protein_coding	ENST00000382905	4	40155

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000167	0.892	125729	0	14	125743	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0553	194	192	1.01	0.00000895	2497
Missense in Polyphen		24	18.801	1.2765		222
Synonymous	-0.628	71	64.6	1.10	0.00000296	732
Loss of Function	1.46	8	13.9	0.577	7.85e-7	172

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000122	0.000119
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000724	0.0000615
Middle Eastern	0.000109	0.000109
South Asian	0.0000725	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Functions as a transcriptional regulator. {ECO:0000269|PubMed:17126306}.

Recessive Scores

• pRec: 0.0705

Intolerance Scores

• loftool: 0.990
• rvis_EVS: 0.49
• rvis_percentile_EVS: 79.38

Haploinsufficiency Scores

• pHI: 0.0675
• hipred: N
• hipred_score: 0.252
• ghis: 0.503

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.824

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zmym5

Gene ontology

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