ZMYM6

protein-coding

zinc finger MYM-type containing 6, the group of Zinc fingers MYM-type

Gene summary

Predicted to enable DNA binding activity. Located in nucleoplasm. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

ZNF258

MANE transcript

NM_007167.4

Inheritance

ClinVar variants

U:134B:26

Top phenotype

ZMYM6-related disorder

gnomAD constraint

pLI —, LoF o/e 0.51

Max pathogenic AF

—

Genomic locus

chr1:34,986,165-35,031,945

External References & Databases

Ensembl (ENSG00000163867)

Transcript & Mutation Effects

hg38 • Region Span ~45.8 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

intellectual disabilityLIMITED

Inheritance Pattern: AD

Disease ID:MONDO:0001071

Submitter: G2P

intellectual disabilityLIMITED

Inheritance Pattern: AD

Disease ID:MONDO:0001071

Submitter: Ambry Genetics

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ZMYM6 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 138

ZMYM6-related disorderTotal: 20

not providedTotal: 5

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_007167.4. 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				7 clinvar	3 clinvar	10
missense			130 clinvar	11 clinvar	5 clinvar	146
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	134	18	8	160

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 51 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_007167.4	RefSeq	NP_009098.3	15	MANE Select
ENST00000357182.9	Ensembl	ENSP00000349708.4	15	MANE Select
ENST00000317538.10	Ensembl	ENSP00000326695.5	3	Standard
ENST00000317538.9	Ensembl	ENSP00000326695.5	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

cytoskeleton organization
multicellular organism development
regulation of cell morphogenesis

Molecular Function

DNA binding
zinc ion binding

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000357182
Coding exons: 15
Length: 48047
Individuals with no LoFs: 125695
Homozygous LoFs: 0
Heterozygous LoFs: 53
Defined: 125748
p: 0.000211

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.70	529	651	0.812	0.0000315	8693
Missense (PolyPhen)		112	177.7	0.63028		2476
Synonymous	2.02	191	230	0.831	0.0000111	2461
Loss of Function	3.47	30	58.7	0.511	0.00000317	821

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.00018	0.00017	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00035	0.00033	rare
Finnish	0.00014	0.00014	rare
European (Non-Finnish)	0.00027	0.00026	rare
South Asian	0.00026	0.00026	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Plays a role in the regulation of cell morphology and cytoskeletal organization. {ECO:0000269|PubMed:21834987}.;

Recessive Scores

pRec: 0.0906

Intolerance Scores

LoFtool: 0.946
RVIS EVS: -0.33
RVIS percentile EVS: 30.9

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.756

Gene Damage Prediction

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