SYP
Basic information
Region (hg38): X:49187815-49200218
Links
Phenotypes
GenCC
Source:
- intellectual disability, X-linked 96 (Limited), mode of inheritance: XL
- non-syndromic X-linked intellectual disability (Supportive), mode of inheritance: XL
- intellectual disability, X-linked 96 (Limited), mode of inheritance: XL
- intellectual disability, X-linked 96 (Limited), mode of inheritance: XL
- non-syndromic X-linked intellectual disability (Moderate), mode of inheritance: XL
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Intellectual developmental disorder, X-linked 96 | XL | 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 | Neurologic | 19377476 |
ClinVar
This is a list of variants' phenotypes submitted to
- Intellectual disability, X-linked 96 (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SYP 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 | 8 | |||||
missense | 40 | 45 | ||||
nonsense | 3 | |||||
start loss | 2 | |||||
frameshift | 2 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 1 | |||||
splice region | 0 | |||||
non coding | 2 | |||||
Total | 1 | 4 | 45 | 10 | 3 |
Variants in SYP
This is a list of pathogenic ClinVar variants found in the SYP region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
X-49191436-A-T | Uncertain significance (Sep 21, 2015) | |||
X-49191477-C-T | Uncertain significance (Jan 21, 2022) | |||
X-49191481-A-G | Uncertain significance (Jan 17, 2023) | |||
X-49191490-G-T | Uncertain significance (Mar 11, 2024) | |||
X-49191493-C-T | Uncertain significance (Oct 02, 2019) | |||
X-49191497-G-C | Intellectual disability, X-linked 96 | Uncertain significance (Mar 29, 2024) | ||
X-49191502-C-T | History of neurodevelopmental disorder • not specified | Conflicting classifications of pathogenicity (Dec 31, 2019) | ||
X-49191510-C-T | not specified | Likely benign (Jul 18, 2013) | ||
X-49191511-C-A | not specified • Inborn genetic diseases | Conflicting classifications of pathogenicity (Nov 01, 2022) | ||
X-49191526-C-T | Uncertain significance (Jun 01, 2022) | |||
X-49191546-TAGTC-T | Intellectual disability, X-linked 96 | Likely pathogenic (Oct 23, 2020) | ||
X-49191578-G-A | not specified | Uncertain significance (Aug 24, 2017) | ||
X-49191592-C-T | Intellectual disability, X-linked 96 | Uncertain significance (Jan 13, 2022) | ||
X-49191593-G-C | Intellectual disability, X-linked 96 | Uncertain significance (Jul 20, 2022) | ||
X-49191618-C-T | Uncertain significance (Dec 10, 2023) | |||
X-49191674-C-G | Benign (Jul 20, 2018) | |||
X-49191691-C-T | Inborn genetic diseases | Likely benign (Jun 28, 2024) | ||
X-49191692-G-A | Conflicting classifications of pathogenicity (Dec 31, 2019) | |||
X-49191695-C-T | Neurodevelopmental delay | Likely pathogenic (-) | ||
X-49191698-G-T | Benign (Dec 31, 2019) | |||
X-49191725-G-T | Intellectual disability, X-linked 96 | Uncertain significance (Apr 12, 2023) | ||
X-49191730-C-G | Intellectual disability, X-linked 96 | Pathogenic (May 01, 2009) | ||
X-49191753-A-C | Uncertain significance (May 02, 2022) | |||
X-49191755-G-A | Likely benign (Aug 01, 2021) | |||
X-49193270-A-G | Intellectual disability, X-linked 96 | Likely pathogenic (-) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
SYP | protein_coding | protein_coding | ENST00000263233 | 6 | 12450 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.915 | 0.0844 | 121170 | 1 | 0 | 121171 | 0.00000413 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 1.33 | 87 | 130 | 0.670 | 0.00000990 | 2019 |
Missense in Polyphen | 19 | 52.4 | 0.36259 | 874 | ||
Synonymous | -1.09 | 71 | 60.3 | 1.18 | 0.00000508 | 633 |
Loss of Function | 2.99 | 1 | 12.3 | 0.0811 | 9.32e-7 | 168 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00 | 0.00 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.00 | 0.00 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.00 | 0.00 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.0000533 | 0.0000333 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Possibly involved in structural functions as organizing other membrane components or in targeting the vesicles to the plasma membrane. Involved in the regulation of short-term and long-term synaptic plasticity (By similarity). {ECO:0000250}.;
- Disease
- DISEASE: Mental retardation, X-linked 96 (MRX96) [MIM:300802]: A disorder characterized by significantly below average general intellectual functioning associated with impairments in adaptive behavior and manifested during the developmental period. {ECO:0000269|PubMed:19377476}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
- Pathway
- Synaptic Vesicle Pathway
(Consensus)
Recessive Scores
- pRec
- 0.652
Intolerance Scores
- loftool
- 0.0918
- rvis_EVS
- -0.14
- rvis_percentile_EVS
- 42.88
Haploinsufficiency Scores
- pHI
- 0.392
- hipred
- Y
- hipred_score
- 0.743
- ghis
- 0.569
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.829
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Syp
- Phenotype
- normal phenotype; 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);
Gene ontology
- Biological process
- endocytosis;synaptic vesicle maturation;regulation of long-term neuronal synaptic plasticity;regulation of short-term neuronal synaptic plasticity;synaptic vesicle endocytosis;synaptic vesicle membrane organization;cellular response to organic substance;regulation of synaptic vesicle exocytosis;regulation of opioid receptor signaling pathway
- Cellular component
- synaptic vesicle;cell junction;integral component of synaptic vesicle membrane;neuromuscular junction;presynaptic membrane;neuron projection;terminal bouton;presynaptic active zone;excitatory synapse;Schaffer collateral - CA1 synapse
- Molecular function
- cholesterol binding;SH2 domain binding;identical protein binding;protein self-association