SS18

protein-coding

SS18 subunit of BAF chromatin remodeling complex, the group of BAF complex|GBAF complex

Gene summary

Enables transcription coactivator activity. Involved in positive regulation of transcription by RNA polymerase II. Part of SWI/SNF complex. Implicated in synovial sarcoma. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

SSXT

MANE transcript

NM_001007559.3

Inheritance

—

ClinVar variants

U:44B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.19

Max pathogenic AF

—

Genomic locus

chr18:26,016,253-26,091,217

External References & Databases

Ensembl (ENSG00000141380)

Transcript & Mutation Effects

hg38 • Region Span ~75.0 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SS18 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 39

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001007559.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	1 clinvar		2
missense			38 clinvar	1 clinvar		39
nonsense			2 clinvar			2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	44	2	0	46

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 69 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001007559.3	RefSeq	NP_001007560.1	11	MANE Select
ENST00000415083.7	Ensembl	ENSP00000414516.2	11	MANE Select
NM_001308201.2	RefSeq	NP_001295130.1	10	Standard
NM_005637.4	RefSeq	NP_005628.2	10	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Transcriptional misregulation in cancer - Homo sapiens (human)

Biological Process

microtubule cytoskeleton organization
cell morphogenesis
intracellular signal transduction
response to drug
positive regulation of transcription, DNA-templated

Molecular Function

protein binding
nuclear receptor transcription coactivator activity

Cellular Component

nucleus
cytoplasmic microtubule
SWI/SNF complex
npBAF complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000415083
Coding exons: 11
Length: 74604
Individuals with no LoFs: 125739
Homozygous LoFs: 0
Heterozygous LoFs: 9
Defined: 125748
p: 0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.06	191	237	0.807	0.0000110	2768
Missense (PolyPhen)		39	58.484	0.66685		683
Synonymous	1.20	61	74.2	0.822	0.00000395	699
Loss of Function	4.15	6	30.9	0.194	0.00000133	320

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000035	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0.00014	0.00014	rare
European (Non-Finnish)	0.000029	0.000026	rare
South Asian	0.000035	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Appears to function synergistically with RBM14 as a transcriptional coactivator. Isoform 1 and isoform 2 function in nuclear receptor coactivation. Isoform 1 and isoform 2 function in general transcriptional coactivation. Component of SWI/SNF chromatin remodeling subcomplex GBAF that carries out key enzymatic activities, changing chromatin structure by altering DNA-histone contacts within a nucleosome in an ATP-dependent manner (PubMed:29374058). {ECO:0000269|PubMed:15919756, ECO:0000269|PubMed:29374058}.;

Recessive Scores

pRec: 0.121

Intolerance Scores

RVIS EVS: -0.12
RVIS percentile EVS: 45.13

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): K
Indispensability pred.: E
Indispensability score: 0.550

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium