Menu
GeneBe

SCAMP1

secretory carrier membrane protein 1, the group of Secretory carrier membrane proteins

Basic information

Region (hg38): 5:78360610-78480739

Links

ENSG00000085365NCBI:9522OMIM:606911HGNC:10563Uniprot:O15126AlphaFoldGenCCjaxSfariGnomADPubmed

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SCAMP1 gene.

  • Inborn genetic diseases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SCAMP1 gene is commonly pathogenic or not.

Variant type Pathogenic Likely pathogenic VUS Likely benign Benign Sum
synonymous 0
missense 1 1
nonsense 0
start loss 0
frameshift 0
inframe indel 0
splice variant 0
non coding 0
Total 0 0 1 0 0

Variants in SCAMP1

This is a list of pathogenic ClinVar variants found in the SCAMP1 region.

Position Type Phenotype Significance ClinVar
5-78418852-A-G Inborn genetic diseases Uncertain significance (May 18, 2023)link
5-78421854-G-A Inborn genetic diseases Uncertain significance (Aug 09, 2021)link

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SCAMP1protein_codingprotein_codingENST00000538629 9120224
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.9770.0230123037011230380.00000406
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense2.42761630.4670.000007982202
Missense in Polyphen2159.0370.35571824
Synonymous1.184556.20.8010.00000295626
Loss of Function3.47116.00.06267.67e-7206

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.000008950.00000895
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Functions in post-Golgi recycling pathways. Acts as a recycling carrier to the cell surface.;
Pathway
miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;Neutrophil degranulation;Innate Immune System;Immune System;Fibroblast growth factor-1 (Consensus)

Recessive Scores

pRec
0.107

Haploinsufficiency Scores

pHI
0.929
hipred
Y
hipred_score
0.731
ghis

Essentials

essential_gene_CRISPR
essential_gene_CRISPR2
essential_gene_gene_trap
gene_indispensability_pred
E
gene_indispensability_score
0.876

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Scamp1
Phenotype
normal phenotype; cellular phenotype;

Gene ontology

Biological process
post-Golgi vesicle-mediated transport;protein transport;neutrophil degranulation
Cellular component
Golgi membrane;Golgi apparatus;trans-Golgi network;plasma membrane;integral component of membrane;clathrin-coated vesicle;synaptic vesicle membrane;trans-Golgi network membrane;specific granule membrane;zymogen granule membrane;recycling endosome membrane
Molecular function
protein binding