MTMR10

Chr 15AR

myotubularin related protein 10

NCBI Gene: 54893ENSG00000166912UniProt: Q9NXD2

Predicted to enable phosphatidylinositol-3-phosphate phosphatase activity. Predicted to be involved in phosphatidylinositol dephosphorylation. Located in cytoplasm. [provided by Alliance of Genome Resources, Jul 2025]

Primary Disease Associations & Inheritance

Short-rib thoracic dysplasia 1 with or without polydactylyMIM #208500
AR
606
ClinVar variants
90
Pathogenic / LP
0.00
pLI score
0
Active trials
Clinical Summary— MTMR10
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
90 Pathogenic / Likely Pathogenic· 136 VUS of 606 total submissions
Some data sources returned errors (1)

clinvar: Error: NCBI fetch failed: 429 https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.
0.68LOEUF
pLI 0.000
Z-score 3.17
OE 0.46 (0.31–0.68)
Tolerant

Typical tolerance to LoF variation

Missense Constraint?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.
1.27Z-score
OE missense 0.82 (0.75–0.90)
318 obs / 388.4 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.
LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.0.46 (0.31–0.68)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.82 (0.75–0.90)
0≤0.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.1.09
0≤1.21.6
LoF obs/exp: 18 / 39.5Missense obs/exp: 318 / 388.4Syn Z: -0.85

ClinVar Variant Classifications

606 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic82
Likely Pathogenic8
VUS136
Likely Benign36
Benign4
Conflicting2
82
Pathogenic
8
Likely Pathogenic
136
VUS
36
Likely Benign
4
Benign
2
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
2
0
80
0
82
Likely Pathogenic
2
0
6
0
8
VUS
0
114
22
0
136
Likely Benign
0
5
6
25
36
Benign
1
1
1
1
4
Conflicting
—2
Total512011526268

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

View in ClinVar →

Protein Context — Lollipop Plot

MTMR10 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

OMIM — Genotype-Phenotype Relationships

1 OMIM entry

OMIM

Short-rib thoracic dysplasia 1 with or without polydactyly

MIM #208500

Disorder mapped to chromosomal region

Autosomal recessive
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
Common and rare variant analyses implicate late-infancy cerebellar development and immune genes in ADHD.
Zhong Y et al.·J Neurodev Disord
2025
Mice with mutations in Trpm1, a gene in the locus of 15q13.3 microdeletion syndrome, display pronounced hyperactivity and decreased anxiety-like behavior.
Hori T et al.·Mol Brain
2021
Prenatal diagnosis of 15q13.3 deletion and duplication syndrome: what do we tell the prospective parents?
Luo X et al.·Arch Gynecol Obstet
2025
Peripheral immune challenges elicit differential up-regulation of hippocampal cytokine and chemokine mRNA expression in a mouse model of the 15q13.3 microdeletion syndrome.
McCamy KM et al.·Cytokine
2022Functional
A 15q13.3 homozygous microdeletion associated with a severe neurodevelopmental disorder suggests putative functions of the TRPM1, CHRNA7, and other homozygously deleted genes.
Lepichon JB et al.·Am J Med Genet A
2010Case report
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →

External Resources

Links to major genomics databases and tools