ZMYM5

protein-coding

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

Gene summary

Predicted to enable zinc ion binding activity. Involved in negative regulation of transcription by RNA polymerase II. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

ZNF237

MANE transcript

NM_001142684.2

Inheritance

ClinVar variants

U:56B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.58

Max pathogenic AF

—

Genomic locus

chr13:19,823,482-19,863,649

External References & Databases

Ensembl (ENSG00000132950)

Transcript & Mutation Effects

hg38 • Region Span ~40.2 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

multiple congenital anomalies/dysmorphic syndromeLIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0019042

Submitter: Ambry Genetics

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ZMYM5 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 59

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001142684.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			55 clinvar	4 clinvar		59
nonsense					1 clinvar	1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	56	4	1	61

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 63 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001142684.2	RefSeq	NP_001136156.1	6	MANE Select
ENST00000337963.9	Ensembl	ENSP00000337034.4	6	MANE Select
NM_001039649.3	RefSeq	NP_001034738.1	3	Standard
NM_001039650.3	RefSeq	NP_001034739.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

regulation of transcription by RNA polymerase II
regulation of cell morphogenesis

Molecular Function

DNA-binding transcription factor activity, RNA polymerase II-specific
protein binding
zinc ion binding

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000382905
Coding exons: 4
Length: 40155
Individuals with no LoFs: 125729
Homozygous LoFs: 0
Heterozygous LoFs: 14
Defined: 125743
p: 0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.0553	194	192	1.01	0.00000895	2497
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000064	0.000062	rare
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000072	0.000062	rare
South Asian	0.000073	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.824

Gene Damage Prediction

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