ZMYM1

Chr 1

zinc finger MYM-type containing 1

Also known as: MYM

NCBI Gene: 79830 ENSG00000197056 UniProt: Q5SVZ6

The ZMYM1 protein enables protein dimerization and zinc ion binding in the nucleus. Mutations cause autosomal recessive developmental delay with dysmorphic facies and dental anomalies. This gene is highly constrained against loss-of-function variants, suggesting complete loss of function is likely incompatible with normal development.

ResearchSummary from RefSeq

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]

ResearchGenerating clinical summary…

DNmechanismLOEUF 0.66

Clinical Summary— ZMYM1

⚡

Population Constraint (gnomAD)

Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.

📋

ClinVar Variants

118 VUS of 139 total submissions

Explore recent and relevant literature in Research Assistant →

Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

0.66LOEUF

pLI 0.000

Z-score 3.38

OE 0.46 (0.33–0.66)

Tolerant

Typical tolerance to LoF variation

Missense Constraint?

1.50Z-score

OE missense 0.82 (0.76–0.89)

460 obs / 560.0 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.46 (0.33–0.66)

0≤0.351.4

Missense OE?0.82 (0.76–0.89)

0≤0.61.4

Synonymous OE?0.95

0≤1.21.6

LoF obs/exp: 21 / 45.6Missense obs/exp: 460 / 560.0Syn Z: 0.61

This gene — mechanism propensity

0.6358th %ile

GOF

0.4381th %ile

LOF

0.3260th %ile

The highest-scoring mechanism for this gene is dominant-negative.

DNprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

139 submitted variants in ClinVar

ClinVar

Classification Summary

VUS118

Likely Benign6

118

VUS

Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	Missense + Inframe	Total
Pathogenic	0	0
Likely Pathogenic	0	0
VUS	118	118
Likely Benign	6	6
Benign	0	0
Total	124	124

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

9 pathogenic / likely-pathogenic (of 16) ClinVar copy-number / structural variants overlap ZMYM1 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →