SLC17A5
Basic information
Region (hg38): 6:73593379-73653992
Previous symbols: [ "SIASD" ]
Links
Phenotypes
GenCC
Source:
- Salla disease (Definitive), mode of inheritance: AR
- Salla disease (Strong), mode of inheritance: AR
- free sialic acid storage disease, infantile form (Strong), mode of inheritance: AR
- free sialic acid storage disease, infantile form (Supportive), mode of inheritance: AR
- intermediate severe Salla disease (Supportive), mode of inheritance: AR
- Salla disease (Supportive), mode of inheritance: AR
- free sialic acid storage disease, infantile form (Strong), mode of inheritance: AR
- free sialic acid storage disease (Definitive), mode of inheritance: AR
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Infantile sialic acid storage disorder; Sialuria, Finnish type (Salla disease) | AR | General | Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing | Biochemical; Cardiovascular; Gastrointestinal; Neurologic | 4043964; 10546100; 10069709; 10581036; 10947946; 12121352; 12794687; 12794688; 15172005; 16170568; 19557856; 20101035; 20301643; 20637281 |
ClinVar
This is a list of variants' phenotypes submitted to
- Salla disease (33 variants)
- not provided (4 variants)
- Sialic acid storage disease, severe infantile type (3 variants)
- Sialic acid storage disease, severe infantile type;Salla disease (3 variants)
- not specified (1 variants)
- Salla disease;Sialic acid storage disease, severe infantile type (1 variants)
- Inborn genetic diseases (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC17A5 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 | 161 | 163 | ||||
missense | 11 | 133 | 146 | |||
nonsense | 12 | 22 | 37 | |||
start loss | 5 | |||||
frameshift | 17 | 42 | 63 | |||
inframe indel | 4 | |||||
splice donor/acceptor (+/-2bp) | 22 | 25 | ||||
splice region | 1 | 8 | 31 | 40 | ||
non coding | 28 | 74 | 55 | 157 | ||
Total | 35 | 100 | 172 | 236 | 57 |
Highest pathogenic variant AF is 0.000453
Variants in SLC17A5
This is a list of pathogenic ClinVar variants found in the SLC17A5 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
6-73593381-A-G | Salla disease • Sialic acid storage disease, severe infantile type | Uncertain significance (Jan 13, 2018) | ||
6-73593385-C-T | Salla disease • Sialic acid storage disease, severe infantile type | Uncertain significance (Jan 12, 2018) | ||
6-73593447-C-A | Salla disease • Sialic acid storage disease, severe infantile type | Conflicting classifications of pathogenicity (Jan 13, 2018) | ||
6-73593489-TA-T | Salla disease | Uncertain significance (Jun 14, 2016) | ||
6-73593511-C-T | Salla disease • Sialic acid storage disease, severe infantile type | Uncertain significance (Jan 12, 2018) | ||
6-73593512-G-A | Salla disease • Sialic acid storage disease, severe infantile type | Uncertain significance (Jan 13, 2018) | ||
6-73593544-T-C | Salla disease • Sialic acid storage disease, severe infantile type | Uncertain significance (Jan 12, 2018) | ||
6-73593585-G-C | Salla disease • Sialic acid storage disease, severe infantile type | Conflicting classifications of pathogenicity (Jan 13, 2018) | ||
6-73593627-C-T | Salla disease • Sialic acid storage disease, severe infantile type | Uncertain significance (Jan 12, 2018) | ||
6-73593744-TA-T | Salla disease | Uncertain significance (Jun 14, 2016) | ||
6-73593745-A-T | Salla disease • Sialic acid storage disease, severe infantile type | Uncertain significance (Jan 13, 2018) | ||
6-73593871-C-T | Salla disease • Sialic acid storage disease, severe infantile type | Uncertain significance (Jan 13, 2018) | ||
6-73593922-A-T | Salla disease • Sialic acid storage disease, severe infantile type | Uncertain significance (Jan 13, 2018) | ||
6-73594021-T-C | Sialic acid storage disease, severe infantile type • Salla disease | Uncertain significance (Jan 12, 2018) | ||
6-73594106-C-T | Salla disease • Sialic acid storage disease, severe infantile type | Benign (Jan 13, 2018) | ||
6-73594168-G-A | Sialic acid storage disease, severe infantile type • Salla disease | Benign (Jan 12, 2018) | ||
6-73594176-G-A | Salla disease • Sialic acid storage disease, severe infantile type | Uncertain significance (Jan 12, 2018) | ||
6-73594240-G-A | Salla disease • Sialic acid storage disease, severe infantile type | Uncertain significance (Jan 12, 2018) | ||
6-73594260-C-T | Salla disease • Sialic acid storage disease, severe infantile type | Uncertain significance (Jan 12, 2018) | ||
6-73594278-A-G | Salla disease • Sialic acid storage disease, severe infantile type | Likely benign (Jan 13, 2018) | ||
6-73594313-C-T | Sialic acid storage disease, severe infantile type • Salla disease | Benign (Jan 12, 2018) | ||
6-73594315-G-A | Salla disease • Sialic acid storage disease, severe infantile type | Uncertain significance (Jan 12, 2018) | ||
6-73594411-G-A | Salla disease • Sialic acid storage disease, severe infantile type | Uncertain significance (Jan 13, 2018) | ||
6-73594482-G-C | Salla disease • Sialic acid storage disease, severe infantile type | Uncertain significance (Jan 13, 2018) | ||
6-73594489-C-T | Sialic acid storage disease, severe infantile type • Salla disease | Likely benign (Jan 13, 2018) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
SLC17A5 | protein_coding | protein_coding | ENST00000355773 | 11 | 60777 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
6.85e-10 | 0.668 | 125648 | 0 | 100 | 125748 | 0.000398 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.714 | 230 | 263 | 0.876 | 0.0000128 | 3179 |
Missense in Polyphen | 78 | 101.01 | 0.77217 | 1167 | ||
Synonymous | 0.565 | 88 | 95.0 | 0.926 | 0.00000478 | 1000 |
Loss of Function | 1.39 | 18 | 25.6 | 0.704 | 0.00000118 | 309 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000796 | 0.000796 |
Ashkenazi Jewish | 0.0000992 | 0.0000992 |
East Asian | 0.000218 | 0.000217 |
Finnish | 0.000141 | 0.000139 |
European (Non-Finnish) | 0.000551 | 0.000545 |
Middle Eastern | 0.000218 | 0.000217 |
South Asian | 0.0000980 | 0.0000980 |
Other | 0.000676 | 0.000652 |
dbNSFP
Source:
- Function
- FUNCTION: Transports glucuronic acid and free sialic acid out of the lysosome after it is cleaved from sialoglycoconjugates undergoing degradation, this is required for normal CNS myelination. Mediates aspartate and glutamate membrane potential- dependent uptake into synaptic vesicles and synaptic-like microvesicles. Also functions as an electrogenic 2NO(3)(-)/H(+) cotransporter in the plasma membrane of salivary gland acinar cells, mediating the physiological nitrate efflux, 25% of the circulating nitrate ions is typically removed and secreted in saliva. {ECO:0000269|PubMed:10581036, ECO:0000269|PubMed:11751519, ECO:0000269|PubMed:15510212, ECO:0000269|PubMed:21781115, ECO:0000269|PubMed:22778404}.;
- Disease
- DISEASE: Infantile sialic acid storage disorder (ISSD) [MIM:269920]: Severe form of sialic acid storage disease. Affected newborns exhibit visceromegaly, coarse features and failure to thrive immediately after birth. These patients have a shortened life span, usually less than 2 years. {ECO:0000269|PubMed:10581036, ECO:0000269|PubMed:10947946}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
- Pathway
- Lysosome - Homo sapiens (human);Sialuria or French Type Sialuria;Sialuria or French Type Sialuria;Amino Sugar Metabolism;G(M2)-Gangliosidosis: Variant B, Tay-sachs disease;Tay-Sachs Disease;Salla Disease/Infantile Sialic Acid Storage Disease;Post-translational protein modification;Metabolism of proteins;Organic anion transporters;Amino acid and oligopeptide SLC transporters;Transport of inorganic cations/anions and amino acids/oligopeptides;SLC-mediated transmembrane transport;Transport of small molecules;Phosphatidylinositol phosphate metabolism;Aminosugars metabolism;Sialic acid metabolism;Synthesis of substrates in N-glycan biosythesis;Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein;Asparagine N-linked glycosylation
(Consensus)
Recessive Scores
- pRec
- 0.256
Intolerance Scores
- loftool
- 0.882
- rvis_EVS
- 0.06
- rvis_percentile_EVS
- 58.85
Haploinsufficiency Scores
- pHI
- 0.187
- hipred
- Y
- hipred_score
- 0.704
- ghis
- 0.485
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.514
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | High | High | High |
Primary Immunodeficiency | High | High | High |
Cancer | High | High | High |
Mouse Genome Informatics
- Gene name
- Slc17a5
- Phenotype
- growth/size/body region phenotype; homeostasis/metabolism phenotype; cellular phenotype; vision/eye 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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); hearing/vestibular/ear phenotype;
Gene ontology
- Biological process
- ion transport;anion transport;amino acid transport;response to bacterium;sialic acid transport;carbohydrate transmembrane transport;proton transmembrane transport
- Cellular component
- lysosome;lysosomal membrane;cytosol;plasma membrane;integral component of plasma membrane;membrane;integral component of membrane;cell junction;synaptic vesicle membrane
- Molecular function
- carbohydrate:proton symporter activity;sialic acid transmembrane transporter activity;sialic acid:proton symporter activity