SMN1 survival of motor neuron 1, telomeric [Homo sapiens (human)] - Gene

Summary

Official Symbol: SMN1provided by HGNC
Official Full Name: survival of motor neuron 1, telomericprovided by HGNC
Primary source: HGNC:HGNC:11117
See related: Ensembl:ENSG00000172062 MIM:600354; AllianceGenome:HGNC:11117
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: SMA; SMN; SMA1; SMA2; SMA3; SMA4; SMA@; SMNT; BCD541; GEMIN1; TDRD16A; T-BCD541
Summary: This gene is part of a 500 kb inverted duplication on chromosome 5q13. This duplicated region contains at least four genes and repetitive elements which make it prone to rearrangements and deletions. The repetitiveness and complexity of the sequence have also caused difficulty in determining the organization of this genomic region. The telomeric and centromeric copies of this gene are nearly identical and encode the same protein. However, mutations in this gene, the telomeric copy, are associated with spinal muscular atrophy; mutations in the centromeric copy do not lead to disease. The centromeric copy may be a modifier of disease caused by mutation in the telomeric copy. The critical sequence difference between the two genes is a single nucleotide in exon 7, which is thought to be an exon splice enhancer. Note that the nine exons of both the telomeric and centromeric copies are designated historically as exon 1, 2a, 2b, and 3-8. It is thought that gene conversion events may involve the two genes, leading to varying copy numbers of each gene. The protein encoded by this gene localizes to both the cytoplasm and the nucleus. Within the nucleus, the protein localizes to subnuclear bodies called gems which are found near coiled bodies containing high concentrations of small ribonucleoproteins (snRNPs). This protein forms heteromeric complexes with proteins such as SIP1 and GEMIN4, and also interacts with several proteins known to be involved in the biogenesis of snRNPs, such as hnRNP U protein and the small nucleolar RNA binding protein. Multiple transcript variants encoding distinct isoforms have been described. [provided by RefSeq, Jul 2014]
Expression: Ubiquitous expression in bone marrow (RPKM 24.8), testis (RPKM 21.9) and 25 other tissues See more
Orthologs: all
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Genomic context

Location:: 5q13.2

Exon count:: 11

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	5	NC_000005.10 (70924941..70966375)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	5	NC_060929.1 (71381729..71423141)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	5	NC_000005.9 (70220768..70248842)

Chromosome 5 - NC_000005.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Multidisciplinary approach on divergent outcomes in spinal muscular atrophies: comparing DYNC1H1 and SMN1 gene mutations.
Title: Multidisciplinary approach on divergent outcomes in spinal muscular atrophies: comparing DYNC1H1 and SMN1 gene mutations.
Effect of E134K pathogenic mutation of SMN protein on SMN-SmD1 interaction, with implication in spinal muscular atrophy: A molecular dynamics study.
Title: Effect of E134K pathogenic mutation of SMN protein on SMN-SmD1 interaction, with implication in spinal muscular atrophy: A molecular dynamics study.
Rare homozygous disease-associated sequence variants in children with spinal muscular atrophy: a phenotypic description and review of the literature.
Title: Rare homozygous disease-associated sequence variants in children with spinal muscular atrophy: a phenotypic description and review of the literature.
[Analysis of a Chinese pedigree affected with Spinal muscular atrophy due to compound heterozygous variants of SMN gene].
Title: [Analysis of a Chinese pedigree affected with Spinal muscular atrophy due to compound heterozygous variants of SMN gene].
SMN deficiency perturbs monoamine neurotransmitter metabolism in spinal muscular atrophy.
Title: SMN deficiency perturbs monoamine neurotransmitter metabolism in spinal muscular atrophy.
SMN haploinsufficiency promotes ischemia/ reperfusion-induced AKI-to-CKD transition by endoplasmic reticulum stress activation.
Title: SMN haploinsufficiency promotes ischemia/ reperfusion-induced AKI-to-CKD transition by endoplasmic reticulum stress activation.
Deletions of SMNI gene exon 7 and NAIP gene exon 5 in spinal muscular atrophy patients in selected population.
Title: Deletions of SMNI gene exon 7 and NAIP gene exon 5 in spinal muscular atrophy patients in selected population.
SMN regulates GEMIN5 expression and acts as a modifier of GEMIN5-mediated neurodegeneration.
Title: SMN regulates GEMIN5 expression and acts as a modifier of GEMIN5-mediated neurodegeneration.
The Carrier Frequency of Two SMN1 Genes in Parents of Symptomatic Children with SMA and the Significance of SMN1 Exon 8 in Carriers.
Title: The Carrier Frequency of Two SMN1 Genes in Parents of Symptomatic Children with SMA and the Significance of SMN1 Exon 8 in Carriers.
Full-Length SMN Transcript in Extracellular Vesicles as Biomarker in Individuals with Spinal Muscular Atrophy Type 2 Treated with Nusinersen.
Title: Full-Length SMN Transcript in Extracellular Vesicles as Biomarker in Individuals with Spinal Muscular Atrophy Type 2 Treated with Nusinersen.

Submit: New GeneRIF Correction See all GeneRIFs (264)

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Kugelberg-Welander disease MedGen: C0152109 OMIM: 253400 GeneReviews: Spinal Muscular Atrophy	not available
Spinal muscular atrophy MedGen: C0026847 GeneReviews: Spinal Muscular Atrophy	not available
Spinal muscular atrophy, type II MedGen: C0393538 OMIM: 253550 GeneReviews: Spinal Muscular Atrophy	not available
Spinal muscular atrophy, type IV MedGen: C1838230 OMIM: 271150 GeneReviews: Spinal Muscular Atrophy	not available
Werdnig-Hoffmann disease MedGen: C5848259 OMIM: 253300 GeneReviews: Spinal Muscular Atrophy	not available

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Tat	tat	HIV-1 Tat enhances vIL-6-induced angiogenesis and tumorigenesis of fibroblasts and human endothelial cells, which correlates with upregulation of CD31, CD34, SMA, VEGF, b-FGF, and cyclin D1 expression	PubMed
Vpr	vpr	HIV-1 Vpr downregulates SMN1 in HeLa cells within 12 hours of exposure	PubMed
Vpu	vpu	HIV-1 Vpu-expressing U937 monocytes coculture with LX2 stellate cells to upregulate expression of profibrogenic markers COL-1, PCT, SMA-1, VEGF, and MMP2, which is inhibited by MIF treatment	PubMed
matrix	gag	HIV-1 MA-induced upregulation of collagen-I and alpha-SMA expression is dependent on CXCR2 via the Rho/ROCK-1 pathway	PubMed
	gag	Treatment of human stellate cells with HIV-1 MA upregulates the expression of CXCR2, syndecan-2, collagen-I, alpha-SMA, vimentin, and endothelin-1	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SMN1 (e-PCR)
- UniSTS:253711

D5S2463 (e-PCR)
- UniSTS:61210

D5S1946 (e-PCR)
- UniSTS:61211

STS-U18423 (e-PCR)
- UniSTS:106

D5S1556 (e-PCR)
- UniSTS:150384

G20836 (e-PCR)
- UniSTS:8892

A006I11 (e-PCR)
- UniSTS:8893

D5S2798 (e-PCR)
- UniSTS:474073

D5F150S1 (e-PCR)
- UniSTS:156649

D5F151S1 (e-PCR)
- UniSTS:156650

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables RNA binding	IEA Inferred from Electronic Annotation more info
enables identical protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in DNA-templated transcription termination	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in nervous system development	IEA Inferred from Electronic Annotation more info
involved_in spliceosomal complex assembly	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in spliceosomal complex assembly	NAS Non-traceable Author Statement more info	PubMed
involved_in spliceosomal snRNP assembly	EXP Inferred from Experiment more info	PubMed
involved_in spliceosomal snRNP assembly	IBA Inferred from Biological aspect of Ancestor more info
involved_in spliceosomal snRNP assembly	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
is_active_in Cajal body	IBA Inferred from Biological aspect of Ancestor more info
located_in Cajal body	IDA Inferred from Direct Assay more info	PubMed
is_active_in Gemini of coiled bodies	IBA Inferred from Biological aspect of Ancestor more info
located_in Gemini of coiled bodies	IDA Inferred from Direct Assay more info	PubMed
part_of SMN complex	IBA Inferred from Biological aspect of Ancestor more info
part_of SMN complex	IDA Inferred from Direct Assay more info	PubMed
part_of SMN complex	IPI Inferred from Physical Interaction more info	PubMed
part_of SMN-Sm protein complex	IDA Inferred from Direct Assay more info	PubMed
located_in Z disc	IEA Inferred from Electronic Annotation more info
located_in axon	IEA Inferred from Electronic Annotation more info
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasmic ribonucleoprotein granule	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	TAS Traceable Author Statement more info
located_in neuron projection	IDA Inferred from Direct Assay more info	PubMed
located_in nuclear body	IDA Inferred from Direct Assay more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in nucleoplasm	TAS Traceable Author Statement more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in perikaryon	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: survival motor neuron protein

Names: component of gems 1; gemin-1; survival motor neuron 1 protein; tudor domain containing 16A

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_008691.1 RefSeqGene

Range

5001..33072

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_676

mRNA and Protein(s)

NM_000344.4 → NP_000335.1 survival motor neuron protein isoform d

See identical proteins and their annotated locations for NP_000335.1

Status: REVIEWED

Description

Transcript Variant: This variant (d) represents the longest transcript and encodes the longest isoform (d). This variant is thought to be the predominant transcript produced by this copy of the gene.

Source sequence(s)

AC044797, AC139834, BC062723

Consensus CDS

CCDS34181.1

UniProtKB/Swiss-Prot

A8K0V4, Q13119, Q16637, Q549U5, Q96J51

Related

ENSP00000370083.4, ENST00000380707.9

Conserved Domains (1) summary

pfam06003
Location:27 → 291

SMN; Survival motor neuron protein (SMN)
NM_001297715.1 → NP_001284644.1 survival motor neuron protein isoform a

See identical proteins and their annotated locations for NP_001284644.1

Status: REVIEWED

Description

Transcript Variant: This variant (a) lacks the penultimate exon, which results in an alternate translation stop codon, compared to variant d. The resulting isoform (a) is shorter and has a distinct C-terminus, compared to isoform d.

Source sequence(s)

AC044797, AC139834

Consensus CDS

CCDS75256.1

Related

ENSP00000424926.1, ENST00000506163.5

Conserved Domains (1) summary

pfam06003
Location:27 → 278

SMN; Survival motor neuron protein (SMN)
NM_022874.2 → NP_075012.1 survival motor neuron protein isoform b

See identical proteins and their annotated locations for NP_075012.1

Status: REVIEWED

Description

Transcript Variant: This variant (b) lacks an alternate in-frame exon in the 3' CDS compared to variant d. The resulting protein (isoform b) is shorter but has the same N- and C- termini compared to isoform d.

Source sequence(s)

AC139834, BC062723

Consensus CDS

CCDS34182.1

Conserved Domains (1) summary

pfam06003
Location:27 → 259

SMN; Survival motor neuron protein (SMN)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000005.10 Reference GRCh38.p14 Primary Assembly

Range

70924941..70966375

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047417615.1 → XP_047273571.1 survival motor neuron protein isoform X1
XM_017009786.2 → XP_016865275.1 survival motor neuron protein isoform X4

Conserved Domains (2) summary

smart00333
Location:90 → 147

TUDOR; Tudor domain

pfam06003
Location:27 → 246

SMN; Survival motor neuron protein (SMN)
XM_011543597.2 → XP_011541899.1 survival motor neuron protein isoform X5

See identical proteins and their annotated locations for XP_011541899.1

UniProtKB/TrEMBL

B4DP61

Related

ENSP00000423298.1, ENST00000514951.5

Conserved Domains (1) summary

pfam06003
Location:27 → 224

SMN; Survival motor neuron protein (SMN)
XM_047417618.1 → XP_047273574.1 survival motor neuron protein isoform X6
XM_047417616.1 → XP_047273572.1 survival motor neuron protein isoform X3

Related

ENSP00000428128.1, ENST00000503079.6
XM_011543596.2 → XP_011541898.1 survival motor neuron protein isoform X2

See identical proteins and their annotated locations for XP_011541898.1

UniProtKB/TrEMBL

E7EQZ4

Related

ENSP00000486539.1, ENST00000625245.2

Conserved Domains (2) summary

smart00333
Location:90 → 147

TUDOR; Tudor domain

pfam06003
Location:27 → 278

SMN; Survival motor neuron protein (SMN)

Reference GRCh38.p14 PATCHES

Genomic

NW_025791777.1 Reference GRCh38.p14 PATCHES

Range

1515739..1557047 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047443291.1 → XP_047299247.1 survival motor neuron protein isoform X1
XM_047443295.1 → XP_047299251.1 survival motor neuron protein isoform X9
XM_047443301.1 → XP_047299257.1 survival motor neuron protein isoform X11
XM_047443298.1 → XP_047299254.1 survival motor neuron protein isoform X10
XM_047443297.1 → XP_047299253.1 survival motor neuron protein isoform X4
XM_047443294.1 → XP_047299250.1 survival motor neuron protein isoform X8
XM_047443303.1 → XP_047299259.1 survival motor neuron protein isoform X13
XM_047443300.1 → XP_047299256.1 survival motor neuron protein isoform X6
XM_047443296.1 → XP_047299252.1 survival motor neuron protein isoform X3
XM_047443292.1 → XP_047299248.1 survival motor neuron protein isoform X7

UniProtKB/Swiss-Prot

A8K0V4, Q13119, Q16637, Q549U5, Q96J51
XM_047443302.1 → XP_047299258.1 survival motor neuron protein isoform X12
XM_047443299.1 → XP_047299255.1 survival motor neuron protein isoform X5

UniProtKB/TrEMBL

B4DP61
XM_047443293.1 → XP_047299249.1 survival motor neuron protein isoform X2

UniProtKB/TrEMBL

E7EQZ4

Reference GRCh38.p14 ALT_REF_LOCI_1

Genomic

NW_003315917.2 Reference GRCh38.p14 ALT_REF_LOCI_1

Range

439160..485846 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054329540.1 → XP_054185515.1 survival motor neuron protein isoform X1
XM_054329545.1 → XP_054185520.1 survival motor neuron protein isoform X14
XM_054329544.1 → XP_054185519.1 survival motor neuron protein isoform X6
XM_054329543.1 → XP_054185518.1 survival motor neuron protein isoform X5

UniProtKB/TrEMBL

B4DP61
XM_054329542.1 → XP_054185517.1 survival motor neuron protein isoform X4
XM_054329541.1 → XP_054185516.1 survival motor neuron protein isoform X2

UniProtKB/TrEMBL

E7EQZ4

Reference GRCh38.p14 ALT_REF_LOCI_2

Genomic

NT_187651.1 Reference GRCh38.p14 ALT_REF_LOCI_2

Range

473376..520059

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054329962.1 → XP_054185937.1 survival motor neuron protein isoform X1
XM_054329964.1 → XP_054185939.1 survival motor neuron protein isoform X9
XM_054329966.1 → XP_054185941.1 survival motor neuron protein isoform X10
XM_054329969.1 → XP_054185944.1 survival motor neuron protein isoform X11
XM_054329965.1 → XP_054185940.1 survival motor neuron protein isoform X4
XM_054329967.1 → XP_054185942.1 survival motor neuron protein isoform X5

UniProtKB/TrEMBL

B4DP61
XM_054329968.1 → XP_054185943.1 survival motor neuron protein isoform X6
XM_054329963.1 → XP_054185938.1 survival motor neuron protein isoform X2

UniProtKB/TrEMBL

E7EQZ4

Alternate T2T-CHM13v2.0

Genomic

NC_060929.1 Alternate T2T-CHM13v2.0

Range

71381729..71423141

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054353282.1 → XP_054209257.1 survival motor neuron protein isoform X1
XM_054353284.1 → XP_054209259.1 survival motor neuron protein isoform X15
XM_054353286.1 → XP_054209261.1 survival motor neuron protein isoform X16
XM_054353289.1 → XP_054209264.1 survival motor neuron protein isoform X17
XM_054353285.1 → XP_054209260.1 survival motor neuron protein isoform X4
XM_054353287.1 → XP_054209262.1 survival motor neuron protein isoform X5

UniProtKB/TrEMBL

B4DP61
XM_054353288.1 → XP_054209263.1 survival motor neuron protein isoform X6
XM_054353290.1 → XP_054209265.1 survival motor neuron protein isoform X18
XM_054353291.1 → XP_054209266.1 survival motor neuron protein isoform X19
XM_054353283.1 → XP_054209258.1 survival motor neuron protein isoform X2

UniProtKB/TrEMBL

E7EQZ4