SCAMP3

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

Basic information

Region (hg38): 1:155255978-155262430

Previous symbols: [ "C1orf3" ]

Links

ENSG00000116521 ∙ NCBI:10067 ∙ OMIM:606913 ∙ HGNC:10565 ∙ Uniprot:O14828 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

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			26	1		27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	1	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		not specified	Uncertain significance (Jan 10, 2023)
1-155256328-G-A		not specified	Uncertain significance (Oct 03, 2022)
1-155256361-G-A		not specified	Uncertain significance (Feb 12, 2024)
1-155256395-C-T		not specified	Uncertain significance (Jan 26, 2022)
1-155256400-C-T		not specified	Uncertain significance (Feb 27, 2023)
1-155256413-A-C		not specified	Uncertain significance (Nov 16, 2021)
1-155256675-C-T		not specified	Uncertain significance (Oct 17, 2023)
1-155256676-G-A		not specified	Uncertain significance (Dec 15, 2022)
1-155256723-G-A		not specified	Uncertain significance (Aug 08, 2022)
1-155256724-C-A		not specified	Uncertain significance (Aug 08, 2022)
1-155256724-C-T		not specified	Uncertain significance (Aug 12, 2021)
1-155256732-A-G		not specified	Uncertain significance (Jan 26, 2022)
1-155256759-C-T		not specified	Uncertain significance (Nov 13, 2023)
1-155256765-G-A		not specified	Likely benign (Jan 17, 2024)
1-155256774-A-G		not specified	Uncertain significance (Oct 17, 2023)
1-155257328-G-A		not specified	Uncertain significance (Dec 28, 2023)
1-155257519-C-T		not specified	Uncertain significance (Sep 22, 2023)
1-155257627-A-T		not specified	Uncertain significance (Nov 03, 2022)
1-155258843-A-G		not specified	Uncertain significance (Feb 12, 2024)
1-155258889-T-A		not specified	Uncertain significance (May 17, 2023)
1-155258928-G-A		not specified	Uncertain significance (Dec 13, 2022)
1-155260366-G-C		not specified	Uncertain significance (Nov 12, 2021)
1-155260396-G-A		not specified	Uncertain significance (Dec 22, 2023)
1-155260441-C-G		not specified	Uncertain significance (Apr 18, 2023)
1-155260565-G-A		not specified	Uncertain significance (Aug 13, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SCAMP3	protein_coding	protein_coding	ENST00000302631	9	6452

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00219	0.994	125707	0	41	125748	0.000163

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.381	188	203	0.925	0.0000112	2230
Missense in Polyphen		64	76.91	0.83214		889
Synonymous	0.159	80	81.8	0.978	0.00000455	714
Loss of Function	2.55	8	20.5	0.391	0.00000111	203

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000560	0.000560
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000561	0.0000544
Finnish	0.0000939	0.0000924
European (Non-Finnish)	0.000115	0.000114
Middle Eastern	0.0000561	0.0000544
South Asian	0.000196	0.000196
Other	0.000489	0.000489

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

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Scamp3

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