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GeneBe

SCAMP3

secretory carrier membrane protein 3, the group of Secretory carrier membrane proteins

Basic information

Region (hg38): 1:155255978-155262430

Previous symbols: [ "C1orf3" ]

Links

ENSG00000116521NCBI:10067OMIM:606913HGNC:10565Uniprot:O14828AlphaFoldGenCCjaxSfariGnomADPubmed

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SCAMP3 gene.

  • Inborn genetic diseases (13 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SCAMP3 gene is commonly pathogenic or not.

Variant type Pathogenic Likely pathogenic VUS Likely benign Benign Sum
synonymous 0
missense 13 13
nonsense 0
start loss 0
frameshift 0
inframe indel 0
splice variant 0
non coding 0
Total 0 0 13 0 0

Variants in SCAMP3

This is a list of pathogenic ClinVar variants found in the SCAMP3 region.

Position Type Phenotype Significance ClinVar
1-155256283-C-T Inborn genetic diseases Uncertain significance (Jan 10, 2023)link
1-155256328-G-A Inborn genetic diseases Uncertain significance (Oct 03, 2022)link
1-155256395-C-T Inborn genetic diseases Uncertain significance (Jan 26, 2022)link
1-155256400-C-T Inborn genetic diseases Uncertain significance (Feb 27, 2023)link
1-155256413-A-C Inborn genetic diseases Uncertain significance (Nov 16, 2021)link
1-155256676-G-A Inborn genetic diseases Uncertain significance (Dec 15, 2022)link
1-155256723-G-A Inborn genetic diseases Uncertain significance (Aug 08, 2022)link
1-155256724-C-T Inborn genetic diseases Uncertain significance (Aug 12, 2021)link
1-155256732-A-G Inborn genetic diseases Uncertain significance (Jan 26, 2022)link
1-155257627-A-T Inborn genetic diseases Uncertain significance (Nov 03, 2022)link
1-155258889-T-A Inborn genetic diseases Uncertain significance (May 17, 2023)link
1-155258928-G-A Inborn genetic diseases Uncertain significance (Dec 13, 2022)link
1-155260366-G-C Inborn genetic diseases Uncertain significance (Nov 12, 2021)link
1-155260441-C-G Inborn genetic diseases Uncertain significance (Apr 18, 2023)link
1-155260565-G-A Inborn genetic diseases Uncertain significance (Aug 13, 2021)link
1-155260595-T-G Inborn genetic diseases Uncertain significance (Jun 03, 2022)link
1-155261731-G-A Inborn genetic diseases Uncertain significance (Oct 12, 2021)link

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SCAMP3protein_codingprotein_codingENST00000302631 96452
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.002190.9941257070411257480.000163
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.3811882030.9250.00001122230
Missense in Polyphen6476.910.83214889
Synonymous0.1598081.80.9780.00000455714
Loss of Function2.55820.50.3910.00000111203

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0005600.000560
Ashkenazi Jewish0.000.00
East Asian0.00005610.0000544
Finnish0.00009390.0000924
European (Non-Finnish)0.0001150.000114
Middle Eastern0.00005610.0000544
South Asian0.0001960.000196
Other0.0004890.000489

dbNSFP

Source: dbNSFP

Function
FUNCTION: Functions in post-Golgi recycling pathways. Acts as a recycling carrier to the cell surface.;
Pathway
Fibroblast growth factor-1;EGFR1 (Consensus)

Recessive Scores

pRec
0.112

Intolerance Scores

loftool
0.742
rvis_EVS
0.04
rvis_percentile_EVS
56.92

Haploinsufficiency Scores

pHI
0.206
hipred
Y
hipred_score
0.722
ghis
0.536

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.927

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Scamp3
Phenotype

Gene ontology

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