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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:O15126AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

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 (2 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.

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
2
clinvar
2
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 2 0 0

Variants in SCAMP1

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

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

Position Type Phenotype Significance ClinVar
5-78418852-A-G not specified Uncertain significance (May 18, 2023)2549006
5-78421854-G-A not specified Uncertain significance (Aug 09, 2021)2276042

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