SS18L2

SS18 like 2

Basic information

Region (hg38): 3:42581840-42596934

Links

ENSG00000008324 ∙ NCBI:51188 ∙ OMIM:606473 ∙ HGNC:15593 ∙ Uniprot:Q9UHA2 ∙ 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 SS18L2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SS18L2 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			4			4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	4	0	0

Variants in SS18L2

This is a list of pathogenic ClinVar variants found in the SS18L2 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-42590917-C-T		not specified	Uncertain significance (Sep 24, 2024)
3-42590921-C-A		not specified	Uncertain significance (Nov 15, 2024)
3-42590932-G-C		not specified	Uncertain significance (Jan 17, 2024)
3-42591545-G-T		not specified	Uncertain significance (May 11, 2022)
3-42591564-G-A		not specified	Uncertain significance (Jul 26, 2022)
3-42591597-G-A		not specified	Uncertain significance (Jun 07, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SS18L2	protein_coding	protein_coding	ENST00000447630	3	13275

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0155	0.711	125735	0	13	125748	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.229	41	45.3	0.904	0.00000219	503
Missense in Polyphen		10	10.687	0.93572		154
Synonymous	-0.717	20	16.3	1.23	7.84e-7	137
Loss of Function	0.672	3	4.55	0.660	1.93e-7	50

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000185	0.000185
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000546	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000442	0.0000439
Middle Eastern	0.0000546	0.0000544
South Asian	0.000133	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.102

Intolerance Scores

• loftool: 0.546
• rvis_EVS: 0.1
• rvis_percentile_EVS: 60.96

Haploinsufficiency Scores

• pHI: 0.268
• hipred: N
• hipred_score: 0.231
• ghis: 0.587

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.508

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ss18l2

Gene ontology

• Biological process: positive regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II;positive regulation of dendrite morphogenesis
• Cellular component: nucleus
• Molecular function: transcription coactivator activity