SMN2 survival of motor neuron 2, centromeric [Homo sapiens (human)] - Gene

Summary

Official Symbol: SMN2provided by HGNC
Official Full Name: survival of motor neuron 2, centromericprovided by HGNC
Primary source: HGNC:HGNC:11118
See related: Ensembl:ENSG00000205571 MIM:601627; AllianceGenome:HGNC:11118
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: SMNC; BCD541; GEMIN1; TDRD16B; C-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. While mutations in the telomeric copy are associated with spinal muscular atrophy, mutations in this gene, the centromeric copy, do not lead to disease. This gene 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 full length 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. Four transcript variants encoding distinct isoforms have been described. [provided by RefSeq, Sep 2008]
Expression: Ubiquitous expression in bone marrow (RPKM 24.2), 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 (70049523..70090528)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	5	NC_060929.1 (70791126..70837821, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	5	NC_000005.9 (69345350..69373422)

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
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?

Clinical Phenotype of Pediatric and Adult Patients With Spinal Muscular Atrophy With Four SMN2 Copies: Are They Really All Stable?
Title: Clinical Phenotype of Pediatric and Adult Patients With Spinal Muscular Atrophy With Four SMN2 Copies: Are They Really All Stable?
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.
Newborn screening for spinal muscular atrophy in Osaka -challenges in a Japanese pilot study.
Title: Newborn screening for spinal muscular atrophy in Osaka -challenges in a Japanese pilot study.
A splicing silencer in SMN2 intron 6 is critical in spinal muscular atrophy.
Title: A splicing silencer in SMN2 intron 6 is critical in spinal muscular atrophy.
Effects of Inhibitors of SLC9A-Type Sodium-Proton Exchangers on Survival Motor Neuron 2 (SMN2) mRNA Splicing and Expression.
Title: Effects of Inhibitors of SLC9A-Type Sodium-Proton Exchangers on Survival Motor Neuron 2 (SMN2) mRNA Splicing and Expression.
Revealing diverse alternative splicing variants of the highly homologous SMN1 and SMN2 genes by targeted long-read sequencing.
Title: Revealing diverse alternative splicing variants of the highly homologous SMN1 and SMN2 genes by targeted long-read sequencing.
Spinal Muscular Atrophy - Is Newborn Screening Too Late for Children with Two SMN2 Copies?
Title: Spinal Muscular Atrophy - Is Newborn Screening Too Late for Children with Two SMN2 Copies?
High Concentration or Combined Treatment of Antisense Oligonucleotides for Spinal Muscular Atrophy Perturbed SMN2 Splicing in Patient Fibroblasts.
Title: High Concentration or Combined Treatment of Antisense Oligonucleotides for Spinal Muscular Atrophy Perturbed SMN2 Splicing in Patient Fibroblasts.
SMN protein is required throughout life to prevent spinal muscular atrophy disease progression.
Title: SMN protein is required throughout life to prevent spinal muscular atrophy disease progression.
Identification of SRSF10 as a regulator of SMN2 ISS-N1.
Title: Identification of SRSF10 as a regulator of SMN2 ISS-N1.

Submit: New GeneRIF Correction See all GeneRIFs (154)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

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	Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

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; tudor domain containing 16B

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_008728.1 RefSeqGene

Range

5147..33073

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_677

mRNA and Protein(s)

NM_017411.4 → NP_059107.1 survival motor neuron protein isoform d

See identical proteins and their annotated locations for NP_059107.1

Status: REVIEWED

Description

Transcript Variant: This variant (d) represents the longest transcript and encodes the longest isoform (d).

Source sequence(s)

AI312583, BC015308, CN272420

Consensus CDS

CCDS4007.1

UniProtKB/Swiss-Prot

A8K0V4, Q13119, Q16637, Q549U5, Q96J51

Related

ENSP00000370119.4, ENST00000380743.9

Conserved Domains (1) summary

pfam06003
Location:27 → 291

SMN; Survival motor neuron protein (SMN)
NM_022875.3 → NP_075013.1 survival motor neuron protein isoform a

See identical proteins and their annotated locations for NP_075013.1

Status: REVIEWED

Description

Transcript Variant: This variant (a) lacks an alternate exon in the 3' CDS compared to variant d. The resulting protein (isoform a) is shorter and has a distinct C-terminus compared to isoform d. This variant is thought to be the predominant transcript produced by this copy of the gene.

Source sequence(s)

AA029652, AI312583, BC000908

Consensus CDS

CCDS54867.1

Related

ENSP00000486152.1, ENST00000626847.2

Conserved Domains (1) summary

pfam06003
Location:27 → 278

SMN; Survival motor neuron protein (SMN)
NM_022876.2 → NP_075014.1 survival motor neuron protein isoform b

See identical proteins and their annotated locations for NP_075014.1

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)

AC140134, AI312583, BC015308, CN272420

Consensus CDS

CCDS4008.1

Related

ENSP00000370118.4, ENST00000380742.8

Conserved Domains (1) summary

pfam06003
Location:27 → 259

SMN; Survival motor neuron protein (SMN)
NM_022877.2 → NP_075015.1 survival motor neuron protein isoform c

See identical proteins and their annotated locations for NP_075015.1

Status: REVIEWED

Description

Transcript Variant: This variant (c) lacks two alternate exons in the 3' CDS compared to variant d. The resulting protein (isoform c) is shorter and has a distinct C-terminus compared to isoform d.

Source sequence(s)

AA029652, AC140134, AI312583, BC000908

Conserved Domains (2) summary

smart00333
Location:90 → 147

TUDOR; Tudor domain

pfam06003
Location:27 → 246

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

70049523..70090528

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047417619.1 → XP_047273575.1 survival motor neuron protein isoform X3
XM_047417620.1 → XP_047273576.1 survival motor neuron protein isoform X5
XM_047417621.1 → XP_047273577.1 survival motor neuron protein isoform X6
XM_047417622.1 → XP_047273578.1 survival motor neuron protein isoform X9
XM_011543600.3 → XP_011541902.1 survival motor neuron protein isoform X7

See identical proteins and their annotated locations for XP_011541902.1

UniProtKB/TrEMBL

B4DP61

Related

ENSP00000424282.1, ENST00000511812.5

Conserved Domains (1) summary

pfam06003
Location:27 → 224

SMN; Survival motor neuron protein (SMN)
XM_011543601.2 → XP_011541903.1 survival motor neuron protein isoform X8

See identical proteins and their annotated locations for XP_011541903.1

Conserved Domains (1) summary

pfam06003
Location:27 → 211

SMN; Survival motor neuron protein (SMN)
XM_011543602.4 → XP_011541904.1 survival motor neuron protein isoform X10

See identical proteins and their annotated locations for XP_011541904.1

Conserved Domains (1) summary

pfam06003
Location:27 → 192

SMN; Survival motor neuron protein (SMN)
XM_011543603.4 → XP_011541905.1 survival motor neuron protein isoform X2

See identical proteins and their annotated locations for XP_011541905.1

Conserved Domains (1) summary

pfam06003
Location:27 → 179

SMN; Survival motor neuron protein (SMN)
XM_011543599.2 → XP_011541901.1 survival motor neuron protein isoform X4

See identical proteins and their annotated locations for XP_011541901.1

UniProtKB/TrEMBL

E7EQZ4

Related

ENSP00000486268.1, ENST00000628696.2

Conserved Domains (2) summary

smart00333
Location:90 → 147

TUDOR; Tudor domain

pfam06003
Location:27 → 278

SMN; Survival motor neuron protein (SMN)
XM_017009787.2 → XP_016865276.1 survival motor neuron protein isoform X1

Reference GRCh38.p14 PATCHES

Genomic

NW_025791777.1 Reference GRCh38.p14 PATCHES

Range

809289..850685 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054333028.1 → XP_054189003.1 survival motor neuron protein isoform X3
XM_054333034.1 → XP_054189009.1 survival motor neuron protein isoform X9
XM_054333031.1 → XP_054189006.1 survival motor neuron protein isoform X6
XM_054333030.1 → XP_054189005.1 survival motor neuron protein isoform X5
XM_054333035.1 → XP_054189010.1 survival motor neuron protein isoform X10
XM_054333033.1 → XP_054189008.1 survival motor neuron protein isoform X8
XM_054333032.1 → XP_054189007.1 survival motor neuron protein isoform X7

UniProtKB/TrEMBL

B4DP61
XM_054333029.1 → XP_054189004.1 survival motor neuron protein isoform X4

UniProtKB/TrEMBL

E7EQZ4

Reference GRCh38.p14 ALT_REF_LOCI_2

Genomic

NT_187651.1 Reference GRCh38.p14 ALT_REF_LOCI_2

Range

274862..321547

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054329970.1 → XP_054185945.1 survival motor neuron protein isoform X3
XM_054329973.1 → XP_054185948.1 survival motor neuron protein isoform X5
XM_054329974.1 → XP_054185949.1 survival motor neuron protein isoform X6
XM_054329977.1 → XP_054185952.1 survival motor neuron protein isoform X9
XM_054329975.1 → XP_054185950.1 survival motor neuron protein isoform X7

UniProtKB/TrEMBL

B4DP61
XM_054329976.1 → XP_054185951.1 survival motor neuron protein isoform X8
XM_054329978.1 → XP_054185953.1 survival motor neuron protein isoform X10
XM_054329979.1 → XP_054185954.1 survival motor neuron protein isoform X2
XM_054329971.1 → XP_054185946.1 survival motor neuron protein isoform X4

UniProtKB/TrEMBL

E7EQZ4
XM_054329972.1 → XP_054185947.1 survival motor neuron protein isoform X1

Alternate T2T-CHM13v2.0

Genomic

NC_060929.1 Alternate T2T-CHM13v2.0

Range

70791126..70837821 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054353292.1 → XP_054209267.1 survival motor neuron protein isoform X3
XM_054353299.1 → XP_054209274.1 survival motor neuron protein isoform X9
XM_054353296.1 → XP_054209271.1 survival motor neuron protein isoform X6
XM_054353294.1 → XP_054209269.1 survival motor neuron protein isoform X5
XM_054353301.1 → XP_054209276.1 survival motor neuron protein isoform X2
XM_054353300.1 → XP_054209275.1 survival motor neuron protein isoform X10
XM_054353298.1 → XP_054209273.1 survival motor neuron protein isoform X8
XM_054353297.1 → XP_054209272.1 survival motor neuron protein isoform X7

UniProtKB/TrEMBL

B4DP61
XM_054353295.1 → XP_054209270.1 survival motor neuron protein isoform X11
XM_054353293.1 → XP_054209268.1 survival motor neuron protein isoform X4

UniProtKB/TrEMBL

E7EQZ4