MTMR10

Chr 15AR

myotubularin related protein 10

NCBI Gene: 54893 ENSG00000166912 UniProt: Q9NXD2 OMIM: 208500

The protein functions as a phosphatidylinositol-3-phosphate phosphatase involved in phosphatidylinositol dephosphorylation in the cytoplasm. Mutations cause short-rib thoracic dysplasia 1 with or without polydactyly, a skeletal ciliopathy affecting the thorax and potentially the digits. Inheritance is autosomal recessive.

OMIM ResearchSummary from RefSeq, OMIM

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]

OMIM ResearchGenerating clinical summary…

DNmechanismARLOEUF 0.681 OMIM phenotype

Clinical Summary— MTMR10

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Population Constraint (gnomAD)

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

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ClinVar Variants

27 unique Pathogenic / Likely Pathogenic· 211 VUS of 373 total submissions

Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

0.68LOEUF

pLI 0.000

Z-score 3.17

OE 0.46 (0.31–0.68)

Tolerant

Typical tolerance to LoF variation

Missense Constraint?

1.27Z-score

OE missense 0.82 (0.75–0.90)

318 obs / 388.4 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.46 (0.31–0.68)

0≤0.351.4

Missense OE?0.82 (0.75–0.90)

0≤0.61.4

Synonymous OE?1.09

0≤1.21.6

LoF obs/exp: 18 / 39.5Missense obs/exp: 318 / 388.4Syn Z: -0.85

This gene — mechanism propensity

0.6454th %ile

GOF

0.4777th %ile

LOF

0.3746th %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

373 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic11

Likely Pathogenic16

VUS211

Likely Benign63

Benign37

Conflicting4

Pathogenic

Likely Pathogenic

211

VUS

Likely Benign

Benign

Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	LoF	Missense + Inframe	Non-coding	Synonymous	Total
Pathogenic	10	1	0	0	11
Likely Pathogenic	15	1	0	0	16
VUS	1	198	11	1	211
Likely Benign	0	8	22	33	63
Benign	1	1	31	4	37
Conflicting	—				4
Total	27	209	64	38	342

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

View in ClinVar →

179 pathogenic / likely-pathogenic (of 240) ClinVar copy-number / structural variants overlap MTMR10 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →