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GeneBe

SCAMP2

secretory carrier membrane protein 2, the group of Secretory carrier membrane proteins

Basic information

Region (hg38): 15:74843729-74873365

Links

ENSG00000140497NCBI:10066OMIM:606912HGNC:10564Uniprot:O15127AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SCAMP2 gene.

  • Inborn genetic diseases (12 variants)
  • not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SCAMP2 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
0
missense
12
clinvar
1
clinvar
13
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 12 1 0

Variants in SCAMP2

This is a list of pathogenic ClinVar variants found in the SCAMP2 region.

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

Position Type Phenotype Significance ClinVar
15-74845198-C-T Inborn genetic diseases Uncertain significance (Dec 21, 2022)2412164
15-74845567-A-G Inborn genetic diseases Uncertain significance (Jan 18, 2023)2476294
15-74848697-C-T Inborn genetic diseases Uncertain significance (Aug 10, 2021)2324910
15-74851386-G-A Inborn genetic diseases Uncertain significance (Mar 16, 2022)2278883
15-74852101-C-T Inborn genetic diseases Uncertain significance (Dec 07, 2021)2319864
15-74852122-G-C Inborn genetic diseases Uncertain significance (Dec 06, 2021)2402297
15-74852183-C-T Inborn genetic diseases Uncertain significance (Mar 24, 2023)2529522
15-74854038-T-A Likely benign (Jan 01, 2023)2645551
15-74854064-G-A Inborn genetic diseases Uncertain significance (Jul 13, 2021)2346828
15-74854594-T-C Inborn genetic diseases Uncertain significance (Aug 30, 2022)2309576
15-74854603-G-T Inborn genetic diseases Uncertain significance (Jul 14, 2023)2612196
15-74854632-C-G Inborn genetic diseases Uncertain significance (May 03, 2023)2542716
15-74854648-T-A Inborn genetic diseases Uncertain significance (Apr 05, 2023)2533675

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SCAMP2protein_codingprotein_codingENST00000268099 929636
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.1600.8391257320131257450.0000517
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.301301790.7270.000009702124
Missense in Polyphen3454.7360.62116671
Synonymous0.1857375.00.9730.00000429667
Loss of Function3.00519.20.2619.93e-7195

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00002890.0000289
Ashkenazi Jewish0.000.00
East Asian0.00005440.0000544
Finnish0.000.00
European (Non-Finnish)0.00007970.0000791
Middle Eastern0.00005440.0000544
South Asian0.00006540.0000653
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Functions in post-Golgi recycling pathways. Acts as a recycling carrier to the cell surface.;
Pathway
Serotonin Transporter Activity;Monoamine Transport;Arf6 trafficking events (Consensus)

Recessive Scores

pRec
0.105

Intolerance Scores

loftool
0.272
rvis_EVS
-0.07
rvis_percentile_EVS
48.35

Haploinsufficiency Scores

pHI
0.223
hipred
Y
hipred_score
0.654
ghis
0.519

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.876

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Scamp2
Phenotype

Gene ontology

Biological process
post-Golgi vesicle-mediated transport;protein transport
Cellular component
Golgi membrane;Golgi apparatus;integral component of membrane;transport vesicle;trans-Golgi network membrane;intracellular membrane-bounded organelle;recycling endosome membrane;extracellular exosome
Molecular function
protein binding