• 1
    Haplo
    Score
  • 0
    Triplo
    Score

Gene Facts External Data Attribution

HGNC Symbol
SYP (HGNC:11506) HGNC Entrez Ensembl OMIM UCSC Uniprot GeneReviews LOVD LSDB ClinVar
HGNC Name
synaptophysin
Gene type
protein-coding gene
Locus type
gene with protein product
Previous symbols
No previous names found
Alias symbols
MRX96
%HI
3.93(Read more about the DECIPHER Haploinsufficiency Index)
pLI
0.92(Read more about gnomAD pLI score)
LOEUF
0.39(Read more about gnomAD LOEUF score)
Cytoband
Xp11.23
Genomic Coordinates
GRCh37/hg19: chrX:49044268-49056652 NCBI Ensembl UCSC
GRCh38/hg38: chrX:49187815-49200193 NCBI Ensembl UCSC
MANE Select Transcript
NM_003179.3 ENST00000263233.9 (Read more about MANE Select)
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}. (Source: Uniprot)

Dosage Sensitivity Summary (Gene)

Dosage ID:
ISCA-7493
Curation Status:
Complete
Issue Type:
Dosage Curation - Gene
Haploinsufficiency:
Little Evidence for Haploinsufficiency (1)
Triplosensitivity:
No Evidence for Triplosensitivity (0)
Last Evaluated:
09/26/2018

Haploinsufficiency (HI) Score Details

HI Score:
1
HI Evidence Strength:
Little Evidence for Haploinsufficiency (Disclaimer)
HI Disease:
  • intellectual disability, X-linked 96 Monarch
HI Evidence:
  • PUBMED: 19377476
    Tarpey et al. (2009): Three SYP truncating variants were found in 1,122 XLMR-affected subjects examined (274_275insA, T92fs*45; 177_178CA>GT, N59_K604K*; and 829_832delGACT, D227fs*59). The first two truncating variants segregate with the disease (combined lod score 1.7). Samples were not available for segregation evaluation on the third mutation. There were no truncating variants in 1,401 controls. A missense variant (649G>C, G217R) found in a single subject with intellectual disability at an amino acid residue that is highly conserved and which segregated with intellectual disability (lod score 1.8) was also thought to be implicated in disease causation.
HI Evidence Comments:
From Tarpey et al. 2009: In the three families with truncating variants, intellectual disability was mild to moderate and there were no consistent additional features, although epilepsy was noted in some individuals. Female carriers had no manifestations. Since only three families from a single report with no consistent clinical features has been reported in the literature an ISCA rating of 1 has been given.
NOTE:

The loss-of-function and triplosensitivity ratings for genes on the X chromosome are made in the context of a male genome to account for the effects of hemizygous duplications or nullizygous deletions. In contrast, disruption of some genes on the X chromosome causes male lethality and the ratings of dosage sensitivity instead take into account the phenotype in female individuals. Factors that may affect the severity of phenotypes associated with X-linked disorders include the presence of variable copies of the X chromosome (i.e. 47,XXY or 45,X) and skewed X-inactivation in females.

Triplosensitivity (TS) Score Details

TS Score:
0
TS Evidence Strength:
No Evidence for Triplosensitivity (Disclaimer)
NOTE:

The loss-of-function and triplosensitivity ratings for genes on the X chromosome are made in the context of a male genome to account for the effects of hemizygous duplications or nullizygous deletions. In contrast, disruption of some genes on the X chromosome causes male lethality and the ratings of dosage sensitivity instead take into account the phenotype in female individuals. Factors that may affect the severity of phenotypes associated with X-linked disorders include the presence of variable copies of the X chromosome (i.e. 47,XXY or 45,X) and skewed X-inactivation in females.

Genomic View

Select assembly: (NC_000023.10) (NC_000023.11)