SS18L1

SS18L1 subunit of BAF chromatin remodeling complex, the group of BAF complex

Basic information

Region (hg38): 20:62143769-62182514

Links

ENSG00000184402 ∙ NCBI:26039 ∙ OMIM:606472 ∙ HGNC:15592 ∙ Uniprot:O75177 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• amyotrophic lateral sclerosis (Moderate), mode of inheritance: AD
• amyotrophic lateral sclerosis (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SS18L1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SS18L1 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				5	5	10
missense			14	1		15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	1	2
non coding			1	1	38	40
Total	0	0	15	7	43

Variants in SS18L1

This is a list of pathogenic ClinVar variants found in the SS18L1 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-62143827-G-A		not specified	Uncertain significance (Jul 13, 2021)
20-62143844-C-T		SS18L1-related disorder	Benign (Jul 15, 2018)
20-62143845-C-T		not specified	Uncertain significance (Aug 21, 2024)
20-62143877-A-C		not specified	Uncertain significance (Sep 25, 2023)
20-62158583-A-G			Benign (May 16, 2021)
20-62158616-C-T			Benign (May 16, 2021)
20-62158733-C-T		not specified	Uncertain significance (Oct 11, 2024)
20-62158746-G-A		SS18L1-related disorder	Likely benign (Jun 11, 2019)
20-62158810-C-A			Benign (May 15, 2021)
20-62159694-C-G			Benign (May 21, 2021)
20-62159697-A-G			Benign (May 15, 2021)
20-62159842-G-A			Benign (May 21, 2021)
20-62159959-G-A		not specified	Uncertain significance (Oct 25, 2024)
20-62160042-T-C			Benign (May 15, 2021)
20-62161244-C-A			Benign (May 16, 2021)
20-62161393-G-A			Benign (May 16, 2021)
20-62161411-C-T			Benign (May 25, 2021)
20-62161437-C-T		not specified	Uncertain significance (Feb 22, 2023)
20-62161451-A-T		not specified	Uncertain significance (Oct 01, 2024)
20-62161539-G-T		not specified	Uncertain significance (Nov 22, 2024)
20-62161573-T-G			Uncertain significance (Jul 01, 2013)
20-62161755-C-A			Benign (May 21, 2021)
20-62162589-C-T			Benign (May 21, 2021)
20-62162763-G-A		not specified	Uncertain significance (Feb 27, 2024)
20-62162838-G-A			Likely benign (Dec 31, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SS18L1	protein_coding	protein_coding	ENST00000331758	11	38719

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.982	0.0177	125529	0	6	125535	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.57	184	254	0.724	0.0000167	2566
Missense in Polyphen		39	77.307	0.50449		776
Synonymous	-1.03	135	121	1.12	0.00000958	726
Loss of Function	4.39	4	29.9	0.134	0.00000148	281

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000549	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000182	0.0000176
Middle Eastern	0.0000549	0.0000544
South Asian	0.0000330	0.0000327
Other	0.000165	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcriptional activator which is required for calcium- dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.104

Intolerance Scores

• loftool: 0.452
• rvis_EVS: -0.53
• rvis_percentile_EVS: 20.7

Haploinsufficiency Scores

• pHI: 0.594
• hipred: Y
• hipred_score: 0.654
• ghis: 0.580

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.942

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ss18l1
• Phenotype: growth/size/body region 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); reproductive system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: chromatin organization;dendrite development;positive regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II;positive regulation of dendrite morphogenesis
• Cellular component: kinetochore;condensed chromosome kinetochore;condensed nuclear chromosome, centromeric region;nucleus;cytosol;nuclear body;nBAF complex
• Molecular function: transcription coactivator activity;protein binding