SSPN
Basic information
Region (hg38): 12:26121991-26299290
Previous symbols: [ "KRAG" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
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 | 3 | |||||
missense | 19 | 20 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 0 | |||||
Total | 0 | 0 | 19 | 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 |
---|---|---|---|---|
12-26122127-G-C | not specified | Uncertain significance (May 15, 2024) | ||
12-26122134-G-C | not specified | Uncertain significance (Jun 24, 2022) | ||
12-26122137-G-A | not specified | Uncertain significance (Jun 02, 2024) | ||
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) | ||
12-26122197-G-C | not specified | Uncertain significance (May 30, 2024) | ||
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) | ||
12-26122290-C-T | not specified | Uncertain significance (Jul 02, 2024) | ||
12-26122319-G-A | not specified | Uncertain significance (Sep 20, 2023) | ||
12-26122344-C-T | not specified | Uncertain significance (Feb 01, 2023) | ||
12-26122347-G-A | not specified | Uncertain significance (May 20, 2024) | ||
12-26122364-G-C | Short sleep, familial natural, 1 | Affects (Aug 14, 2009) | ||
12-26122375-C-T | BHLHE41-related disorder | Likely benign (May 10, 2024) | ||
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) | |||
12-26122496-G-A | not specified | Uncertain significance (Aug 28, 2024) | ||
12-26122499-T-G | not specified | Uncertain significance (Oct 04, 2024) |
GnomAD
Source:
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:
- 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
- Molecular function