ZMYM1

protein-coding

zinc finger MYM-type containing 1, the group of Zinc fingers MYM-type

Gene summary

Predicted to enable protein dimerization activity and zinc ion binding activity. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_024772.5

Inheritance

—

ClinVar variants

U:128B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.46

Max pathogenic AF

—

Genomic locus

chr1:35,032,172-35,118,818

External References & Databases

Ensembl (ENSG00000197056)

Transcript & Mutation Effects

hg38 • Region Span ~86.6 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ZMYM1 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 124

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_024772.5. 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			1 clinvar			1
missense			123 clinvar	6 clinvar		129
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	128	6	0	134

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 72 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_024772.5	RefSeq	NP_079048.3	9	MANE Select
ENST00000359858.9	Ensembl	ENSP00000352920.4	9	MANE Select
NM_001289088.2	RefSeq	NP_001276017.1	9	Standard
NM_001289089.2	RefSeq	NP_001276018.1	9	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
zinc ion binding
protein dimerization activity

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000373330
Coding exons: 9
Length: 56074
Individuals with no LoFs: 125125
Homozygous LoFs: 0
Heterozygous LoFs: 48
Defined: 125173
p: 0.000192

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.50	460	560	0.821	0.0000260	7557
Missense (PolyPhen)		95	158.5	0.59937		2338
Synonymous	0.609	192	203	0.946	0.0000102	2068
Loss of Function	3.38	21	45.6	0.460	0.00000237	658

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00026	0.00026	rare
Latino/Admixed American	0.00020	0.00020	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00022	0.00022	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00017	0.00017	rare
South Asian	0.00037	0.00036	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0914

Intolerance Scores

RVIS EVS: 0.58
RVIS percentile EVS: 82.3

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.204

Gene Damage Prediction

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