SMN1

Chr 5q13.2

survival of motor neuron 1, telomeric

Aliases:: BCD541, SMNT, SMA1, SMA2, SMA3
MANE:: ENST00000380707.9

OMIM: 600354 ↗NCBI: 6606 ↗Ensembl ↗

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Predicted protein structure

AlphaFold predicted structure

SMN1 · Q16637

v62025-08-01

Predicted Aligned Error matrix for SMN1 — diagonal shows residue index, colour shows pairwise prediction confidence (lower is better) — Predicted Aligned Error

Mean pLDDT

66.9/ 100

Low

294 residues

Confidence breakdown

Very high(≥ 90)25%
Confident(70–90)17%
Low(50–70)31%
Very low(< 50)28%

Open interactive 3D viewer

AlphaFold (Jumper et al., 2021) · CC BY 4.0

Clinical relevance (Genomics England PanelApp)

Diagnostic Grade (Green)

Arthrogryposis
BIALLELIC, autosomal or pseudoautosomal
Fetal anomalies
BIALLELIC, autosomal or pseudoautosomal
Hereditary neuropathy
BIALLELIC, autosomal or pseudoautosomal
Hereditary neuropathy or pain disorder
BIALLELIC, autosomal or pseudoautosomal
Paediatric motor neuronopathies
BIALLELIC, autosomal or pseudoautosomal
Spinal muscular atrophy type 1 rare mutation testing
BIALLELIC, autosomal or pseudoautosomal
Limb girdle muscular dystrophies, myofibrillar myopathies and distal myopathies
BIALLELIC, autosomal or pseudoautosomal

Disease associations (Open Targets)

Proximal spinal muscular atrophy type 3
0.81
spinal muscular atrophy, type 1
0.79
spinal muscular atrophy, type III
0.79
spinal muscular atrophy, type II
0.76
Proximal spinal muscular atrophy type 2
0.74
spinal muscular atrophy
0.73
spinal muscular atrophy, type IV
0.71
Proximal spinal muscular atrophy type 4
0.68
proximal spinal muscular atrophy
0.63
neurodegenerative disease
0.54

Score is the Open Targets composite evidence score (0-1). Higher = stronger gene-disease association.

Protein function (UniProt)

Survival motor neuron protein

The SMN complex catalyzes the assembly of small nuclear ribonucleoproteins (snRNPs), the building blocks of the spliceosome, and thereby plays an important role in the splicing of cellular pre-mRNAs (PubMed:18984161, PubMed:9845364). Most spliceosomal snRNPs contain a common set of Sm proteins SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF and SNRPG that assemble in a heptameric protein ring on the Sm site of the small nuclear RNA to form the core snRNP (Sm core) (PubMed:18984161). In the cytosol, the Sm proteins SNRPD1, SNRPD2, SNRPE, SNRPF and SNRPG are trapped in an inactive 6S pICln-Sm complex by the chaperone CLNS1A that controls the assembly of the core snRNP (PubMed:18984161). To assemble core snRNPs, the SMN complex accepts the trapped 5Sm proteins from CLNS1A forming an intermediate (PubMed:18984161). Within the SMN complex, SMN1 acts as a structural backbone and together with GEMIN2 it gathers the Sm complex subunits (PubMed:17178713, PubMed:21816274, PubMed:22101937). Binding of snRNA inside 5Sm ultimately triggers eviction of the SMN complex, thereby allowing binding of SNRPD3 and SNRPB to complete assembly of the core snRNP (PubMed:31799625). Ensures the correct splicing of U12 intron-containing genes that may be important for normal motor and proprioceptive neurons development (PubMed:23063131). Also required for resolving RNA-DNA hybrids created by RNA polymerase II, that form R-loop in transcription terminal regions, an important step in proper transcription termination (PubMed:26700805). May also play a role in the metabolism of small nucleolar ribonucleoprotein (snoRNPs)