SS18L1 SS18L1 subunit of BAF chromatin remodeling complex [Homo sapiens (human)] - Gene

Summary

Official Symbol: SS18L1provided by HGNC
Official Full Name: SS18L1 subunit of BAF chromatin remodeling complexprovided by HGNC
Primary source: HGNC:HGNC:15592
See related: Ensembl:ENSG00000184402 MIM:606472; AllianceGenome:HGNC:15592
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: CREST; LP2261; SMARCL2
Summary: This gene encodes a calcium-responsive transactivator which is an essential subunit of a neuron-specific chromatin-remodeling complex. The structure of this gene is similar to that of the SS18 gene. Mutations in this gene are involved in amyotrophic lateral sclerosis (ALS). Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Sep 2014]
Expression: Ubiquitous expression in skin (RPKM 3.8), brain (RPKM 3.7) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 20q13.33

Exon count:: 16

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	20	NC_000020.11 (62143769..62182514)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	20	NC_060944.1 (63934636..63973390)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	20	NC_000020.10 (60718825..60757570)

Chromosome 20 - NC_000020.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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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?

Identification of a novel MEF2C::SS18L1 fusion in childhood acute B-lymphoblastic leukemia.
Title: Identification of a novel MEF2C::SS18L1 fusion in childhood acute B-lymphoblastic leukemia.
The SS18L1 gene rs2295207 polymorphisms in association with hepatocellular carcinoma.
Title: The SS18L1 gene rs2295207 polymorphisms in association with hepatocellular carcinoma.
Protein expression pattern of calcium-responsive transactivator in early postnatal and adult testes.
Title: Protein expression pattern of calcium-responsive transactivator in early postnatal and adult testes.
calcium-responsive transactivator and certain other amyotrophic lateral sclerosis-linked proteins share several features implicated in amyotrophic lateral sclerosis pathogenesis
Title: Calcium-responsive transactivator (CREST) protein shares a set of structural and functional traits with other proteins associated with amyotrophic lateral sclerosis.
Its mutation causes amyotrophic lateral sclerosis.
Title: Genetic analysis of SS18L1 in French amyotrophic lateral sclerosis.
This study demonistrated that CREST mutations inhibited activity-dependent neurite outgrowth in primary neurons, and CREST associated with the ALS protein FUS.
Title: Exome sequencing to identify de novo mutations in sporadic ALS trios.
Observational study of gene-disease association. (HuGE Navigator)
Title: Association of genetic variants with hemorrhagic stroke in Japanese individuals.
A synovial sarcoma of classic morphology contained a novel t(20;X) SS18L1(strong homology to SS18 on Ch20)/SSX1 fusion transcript in which nucleotide 1216 (exon 10) of SS18L1 was fused in-frame with nucleotide 422 (exon 6) of SSX1.
Title: A novel fusion gene, SS18L1/SSX1, in synovial sarcoma.
analysis of the CREST domain that inhibits dendritic growth in cultured neurons
Title: A multifunctional domain of the calcium-responsive transactivator (CREST) that inhibits dendritic growth in cultured neurons.
SS18 and SS18L1 genes map within co-linear DNA segments that may have evolved through a relatively recent genomic duplication event.
Title: Common origin of the human synovial sarcoma associated SS18 and SS18L1 gene loci.

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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

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

NoName (e-PCR)
- UniSTS:9484

D11S2560 (e-PCR)
- UniSTS:37928

D20S1024 (e-PCR)
- UniSTS:74555

RH44827 (e-PCR)
- UniSTS:87903

D15S1477 (e-PCR)
- UniSTS:474482

RH28300 (e-PCR)
- UniSTS:52350

G20785 (e-PCR)
- UniSTS:59837

A006G17 (e-PCR)
- UniSTS:59838

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables transcription coactivator activity	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
involved_in chromatin organization	IEA Inferred from Electronic Annotation more info
involved_in dendrite development	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of DNA-templated transcription	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of dendrite morphogenesis	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
located_in cytosol	IDA Inferred from Direct Assay more info
located_in kinetochore	IDA Inferred from Direct Assay more info	PubMed
part_of nBAF complex	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
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	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: calcium-responsive transactivator

Names: SS18-like protein 1; SS18L1, nBAF chromatin remodeling complex subunit; SYT homolog 1; synovial sarcoma translocation gene on chromosome 18-like 1

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_034255.1 RefSeqGene

Range

5050..43795

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001301778.2 → NP_001288707.1 calcium-responsive transactivator isoform 2

See identical proteins and their annotated locations for NP_001288707.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) has an additional exon in the 5' region and an alternate splice acceptor site, which results in translation initiation at a downstream AUG start codon, compared to variant 1. The resulting isoform (2) has a shorter N-terminus, compared to isoform 1.

Source sequence(s)

AB014593, AK125656, AL078633, BX640848

UniProtKB/Swiss-Prot

O75177
NM_198935.3 → NP_945173.1 calcium-responsive transactivator isoform 1

See identical proteins and their annotated locations for NP_945173.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes the longer isoform (1).

Source sequence(s)

AB014593, AL078633, BX640848, DC375156

Consensus CDS

CCDS13491.1

UniProtKB/Swiss-Prot

A6NNE3, A8K620, B3KWR8, E1P5H7, O75177, Q5JXJ3, Q6MZV9, Q6NTH3, Q6XYD9, Q8NE69, Q9BR55, Q9H4K6

Related

ENSP00000333012.3, ENST00000331758.8

Conserved Domains (1) summary

pfam05030
Location:14 → 73

SSXT; SSXT protein (N-terminal region)

RNA

NR_125980.3 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (3) has an additional exon and an additional segment in the 5' region and lacks an internal segment in the 3' terminal region, compared to variant 1. This variant is represented as non-coding because the absence of the 3' internal segment renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AB014593, BC068993, BX640848, DC375156
NR_125981.3 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (4) lacks an internal segment in the 3' terminal region, compared to variant 1. This variant is represented as non-coding because the absence of the 3' internal segment renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AB014593, BC034494, BX640848

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_000020.11 Reference GRCh38.p14 Primary Assembly

Range

62143769..62182514

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047440083.1 → XP_047296039.1 calcium-responsive transactivator isoform X2
XM_005260389.4 → XP_005260446.1 calcium-responsive transactivator isoform X1

See identical proteins and their annotated locations for XP_005260446.1

UniProtKB/TrEMBL

B4DSR7

Conserved Domains (1) summary

pfam05030
Location:14 → 73

SSXT; SSXT protein (N-terminal region)
XM_047440084.1 → XP_047296040.1 calcium-responsive transactivator isoform X2
XM_017027784.3 → XP_016883273.1 calcium-responsive transactivator isoform X3
XM_011528767.2 → XP_011527069.1 calcium-responsive transactivator isoform X5

See identical proteins and their annotated locations for XP_011527069.1

UniProtKB/Swiss-Prot

O75177

Conserved Domains (1) summary

pfam05030
Location:46 → 76

SSXT; SSXT protein (N-terminal region)
XM_047440085.1 → XP_047296041.1 calcium-responsive transactivator isoform X4

Related

ENSP00000359885.5, ENST00000370848.8

RNA

XR_007067449.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

NC_060944.1 Alternate T2T-CHM13v2.0

Range

63934636..63973390

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054323321.1 → XP_054179296.1 calcium-responsive transactivator isoform X2
XM_054323320.1 → XP_054179295.1 calcium-responsive transactivator isoform X1

UniProtKB/TrEMBL

B4DSR7
XM_054323322.1 → XP_054179297.1 calcium-responsive transactivator isoform X2
XM_054323323.1 → XP_054179298.1 calcium-responsive transactivator isoform X3
XM_054323325.1 → XP_054179300.1 calcium-responsive transactivator isoform X5
XM_054323324.1 → XP_054179299.1 calcium-responsive transactivator isoform X4

RNA

XR_008485249.1 RNA Sequence

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_015558.3: Suppressed sequence

Description

NM_015558.3: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.