LSM10

Chr 1

LSM10, U7 small nuclear RNA associated

Also known as: MST074, MSTP074

NCBI Gene: 84967 ENSG00000181817 UniProt: Q969L4 OMIM: 617909

LSM10 encodes a protein that binds U7 snRNA and functions in the U7 snRNP complex required for histone 3'-end processing and cell cycle progression from G1 to S phases. Mutations in LSM10 cause microcephaly with or without chorioretinopathy, lymphedema, or mental retardation (MCLMR), an autosomal recessive disorder presenting with primary microcephaly and variable additional features including intellectual disability and ocular abnormalities. The gene shows tolerance to loss-of-function variation with a low probability of haploinsufficiency (pLI = 0.004).

OMIM ResearchSummary from RefSeq, UniProt

Enables U7 snRNA binding activity. Involved in positive regulation of G1/S transition of mitotic cell cycle. Located in Cajal body. Part of U7 snRNP. [provided by Alliance of Genome Resources, Jul 2025]

OMIM ResearchGenerating clinical summary…

LOEUF 1.91

Clinical Summary— LSM10

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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

17 VUS of 20 total submissions

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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.91LOEUF

pLI 0.004

Z-score -0.43

OE 1.31 (0.52–1.91)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

0.47Z-score

OE missense 0.86 (0.71–1.04)

72 obs / 84.1 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?1.31 (0.52–1.91)

0≤0.351.4

Missense OE?0.86 (0.71–1.04)

0≤0.61.4

Synonymous OE?1.07

0≤1.21.6

LoF obs/exp: 3 / 2.3Missense obs/exp: 72 / 84.1Syn Z: -0.30

ClinVar Variant Classifications

20 submitted variants in ClinVar

ClinVar

Classification Summary

VUS17

VUS

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	Missense + Inframe	Total
Pathogenic	0	0
Likely Pathogenic	0	0
VUS	17	17
Likely Benign	0	0
Benign	0	0
Total	17	17

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

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8 pathogenic / likely-pathogenic (of 12) ClinVar copy-number / structural variants overlap LSM10 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →