SSPN

sarcospan

Basic information

Region (hg38): 12:26121990-26299290

Previous symbols: [ "KRAG" ]

Links

ENSG00000123096 ∙ NCBI:8082 ∙ OMIM:601599 ∙ HGNC:11322 ∙ Uniprot:Q14714 ∙ 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 SSPN gene.

• Inborn genetic diseases (14 variants)
• not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SSPN 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				1	2	3
missense			14		1	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	3

Variants in SSPN

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

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

Position	Type	Phenotype	Significance	ClinVar
12-26122134-G-C		not specified	Uncertain significance (Jun 24, 2022)
12-26122151-A-C		not specified	Uncertain significance (Apr 17, 2023)
12-26122178-G-C		not specified	Uncertain significance (Sep 22, 2023)
12-26122181-T-G		not specified	Uncertain significance (Jan 04, 2022)
12-26122192-A-T		BHLHE41-related disorder	Likely benign (Jun 22, 2020)
12-26122193-A-G		not specified	Likely benign (Jan 05, 2022)
12-26122222-C-CGCG		BHLHE41-related disorder	Likely benign (May 22, 2023)
12-26122233-C-T		BHLHE41-related disorder	Benign (Feb 18, 2020)
12-26122251-G-A		not specified	Uncertain significance (Jan 31, 2024)
12-26122283-G-T		not specified	Uncertain significance (Apr 26, 2023)
12-26122319-G-A		not specified	Uncertain significance (Sep 20, 2023)
12-26122344-C-T		not specified	Uncertain significance (Feb 01, 2023)
12-26122364-G-C		Short sleep, familial natural, 1	Affects (Aug 14, 2009)
12-26122399-C-G		BHLHE41-related disorder	Benign (Dec 03, 2019)
12-26122422-G-A		not specified	Uncertain significance (Feb 11, 2022)
12-26122431-A-G		Short sleep, familial natural, 1	Affects (Mar 17, 2020)
12-26122435-G-C			Likely benign (May 08, 2018)
12-26122499-T-G		not specified	Uncertain significance (Nov 15, 2021)
12-26122509-G-A		not specified	Uncertain significance (Oct 30, 2023)
12-26122565-C-T		not specified	Uncertain significance (Sep 17, 2021)
12-26122583-G-T		not specified	Uncertain significance (Aug 23, 2021)
12-26122614-C-T		not specified	Uncertain significance (Mar 24, 2023)
12-26122619-G-A		not specified	Uncertain significance (Aug 14, 2023)
12-26122622-G-A		BHLHE41-related disorder	Benign (Oct 23, 2019)
12-26122632-C-G		not specified	Uncertain significance (Mar 23, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SSPN	protein_coding	protein_coding	ENST00000242729	3	177300

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0396	0.851	125736	0	12	125748	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.971	92	122	0.753	0.00000654	1542
Missense in Polyphen		28	42.194	0.66361		564
Synonymous	1.49	44	58.5	0.752	0.00000371	500
Loss of Function	1.29	3	6.58	0.456	2.78e-7	93

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000185	0.000185
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000527	0.0000527
Middle Eastern	0.00	0.00
South Asian	0.0000980	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the dystrophin-glycoprotein complex (DGC), a complex that spans the muscle plasma membrane and forms a link between the F-actin cytoskeleton and the extracellular matrix. Preferentially associates with the sarcoglycan subcomplex of the DGC.
• Pathway: Pathways in clear cell renal cell carcinoma (Consensus)

Recessive Scores

• pRec: 0.223

Intolerance Scores

• loftool: 0.659
• rvis_EVS: 0.64
• rvis_percentile_EVS: 83.78

Haploinsufficiency Scores

• pHI: 0.348
• hipred: N
• hipred_score: 0.462
• ghis: 0.406

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.823

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sspn
• Phenotype: skeleton phenotype; 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); muscle phenotype; homeostasis/metabolism phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: muscle contraction;cell adhesion
• Cellular component: integral component of plasma membrane;dystrophin-associated glycoprotein complex;cell junction;transport vesicle;sarcolemma;postsynaptic membrane