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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:O14828AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

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 (17 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.

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
17
clinvar
17
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 17 0 0

Variants in SCAMP3

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

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

Position Type Phenotype Significance ClinVar
1-155256283-C-T Inborn genetic diseases Uncertain significance (Jan 10, 2023)2464635
1-155256328-G-A Inborn genetic diseases Uncertain significance (Oct 03, 2022)2315227
1-155256395-C-T Inborn genetic diseases Uncertain significance (Jan 26, 2022)2273081
1-155256400-C-T Inborn genetic diseases Uncertain significance (Feb 27, 2023)2489287
1-155256413-A-C Inborn genetic diseases Uncertain significance (Nov 16, 2021)2259307
1-155256676-G-A Inborn genetic diseases Uncertain significance (Dec 15, 2022)2335388
1-155256723-G-A Inborn genetic diseases Uncertain significance (Aug 08, 2022)2359486
1-155256724-C-T Inborn genetic diseases Uncertain significance (Aug 12, 2021)2298011
1-155256732-A-G Inborn genetic diseases Uncertain significance (Jan 26, 2022)2213034
1-155257627-A-T Inborn genetic diseases Uncertain significance (Nov 03, 2022)2322103
1-155258889-T-A Inborn genetic diseases Uncertain significance (May 17, 2023)2548061
1-155258928-G-A Inborn genetic diseases Uncertain significance (Dec 13, 2022)2334070
1-155260366-G-C Inborn genetic diseases Uncertain significance (Nov 12, 2021)2261196
1-155260441-C-G Inborn genetic diseases Uncertain significance (Apr 18, 2023)2537975
1-155260565-G-A Inborn genetic diseases Uncertain significance (Aug 13, 2021)2244916
1-155260595-T-G Inborn genetic diseases Uncertain significance (Jun 03, 2022)2293974
1-155261731-G-A Inborn genetic diseases Uncertain significance (Oct 12, 2021)2254288

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