SS18

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

Basic information

Region (hg38): 18:26016253-26091217

Previous symbols: [ "SSXT" ]

Links

ENSG00000141380

∙ NCBI:6760 ∙ OMIM:600192 ∙ HGNC:11340 ∙ Uniprot:Q15532 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SS18 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SS18 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			14 clinvar	1 clinvar		15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	1	0

Variants in SS18

This is a list of pathogenic ClinVar variants found in the SS18 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Phenotype	Significance	ClinVar
18-26032455-G-A	not specified	Uncertain significance (Mar 06, 2023)	2494363
18-26032532-C-G	not specified	Uncertain significance (Jan 10, 2022)	2271387
18-26035031-C-T	not specified	Uncertain significance (Dec 14, 2023)	3170288
18-26035050-G-A		Uncertain significance (Feb 02, 2021)	1331678
18-26035879-C-T	not specified	Uncertain significance (Jun 04, 2024)	3322770
18-26038558-C-T	not specified	Uncertain significance (Oct 29, 2021)	2257880
18-26038588-G-A	not specified	Uncertain significance (Mar 29, 2023)	2531249
18-26038599-C-T	not specified	Uncertain significance (Aug 28, 2023)	2621697
18-26038626-T-C	not specified	Uncertain significance (May 24, 2024)	3322767
18-26039368-C-T	not specified	Uncertain significance (Apr 12, 2023)	2513796
18-26039370-T-C	not specified	Uncertain significance (Jul 13, 2022)	2301467
18-26039415-T-C	not specified	Uncertain significance (Apr 11, 2023)	2535922
18-26039451-T-C	not specified	Uncertain significance (Jul 25, 2023)	2588064
18-26052637-C-A	not specified	Likely benign (Jun 09, 2022)	2294756
18-26052643-C-T	not specified	Uncertain significance (Mar 06, 2023)	2460001
18-26052672-T-C	not specified	Uncertain significance (May 02, 2024)	3322768
18-26057649-T-G	not specified	Uncertain significance (Mar 30, 2024)	3322769
18-26057736-T-A	not specified	Uncertain significance (Apr 08, 2022)	2282424
18-26087561-T-C	not specified	Uncertain significance (Jun 24, 2022)	2364937
18-26090514-G-A	not specified	Uncertain significance (Aug 21, 2023)	2596412

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SS18	protein_coding	protein_coding	ENST00000415083	11	74604

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.746	0.254	125739	0	9	125748	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.06	191	237	0.807	0.0000110	2768
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000347	0.0000347
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.000139	0.000139
European (Non-Finnish)	0.0000286	0.0000264
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000349	0.0000327
Other	0.00	0.00

dbNSFP

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}.;
Pathway: Transcriptional misregulation in cancer - Homo sapiens (human) (Consensus)

Recessive Scores

pRec: 0.121

Intolerance Scores

loftool
rvis_EVS: -0.12
rvis_percentile_EVS: 45.13

Haploinsufficiency Scores

pHI: 0.887
hipred: Y
hipred_score: 0.853
ghis: 0.653

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: K
gene_indispensability_pred: E
gene_indispensability_score: 0.550

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Ss18
Phenotype: growth/size/body region phenotype; homeostasis/metabolism phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); embryo phenotype;

Gene ontology

Biological process: microtubule cytoskeleton organization;cell morphogenesis;intracellular signal transduction;response to drug;positive regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II;ephrin receptor signaling pathway;neuronal stem cell population maintenance
Cellular component: nucleus;cytoplasmic microtubule;SWI/SNF complex;npBAF complex
Molecular function: protein binding;nuclear receptor transcription coactivator activity