SCAMP2

secretory carrier membrane protein 2, the group of Secretory carrier membrane proteins

Basic information

Region (hg38): 15:74843729-74873365

Links

ENSG00000140497 ∙ NCBI:10066 ∙ OMIM:606912 ∙ HGNC:10564 ∙ Uniprot:O15127 ∙ 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 SCAMP2 gene.

• Inborn genetic diseases (12 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SCAMP2 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			12	1		13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	1	0

Variants in SCAMP2

This is a list of pathogenic ClinVar variants found in the SCAMP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-74845087-T-C		not specified	Uncertain significance (Sep 29, 2023)
15-74845198-C-T		not specified	Uncertain significance (Dec 21, 2022)
15-74845474-C-T		not specified	Uncertain significance (Dec 17, 2023)
15-74845567-A-G		not specified	Uncertain significance (Jan 18, 2023)
15-74848613-C-G		not specified	Uncertain significance (Nov 17, 2023)
15-74848697-C-T		not specified	Uncertain significance (Aug 10, 2021)
15-74851386-G-A		not specified	Uncertain significance (Mar 16, 2022)
15-74851442-G-A		not specified	Uncertain significance (Jan 24, 2024)
15-74852101-C-T		not specified	Uncertain significance (Dec 07, 2021)
15-74852122-G-C		not specified	Uncertain significance (Dec 16, 2023)
15-74852183-C-T		not specified	Uncertain significance (Mar 24, 2023)
15-74854038-T-A			Likely benign (Jan 01, 2023)
15-74854064-G-A		not specified	Uncertain significance (Jul 13, 2021)
15-74854594-T-C		not specified	Uncertain significance (Aug 30, 2022)
15-74854603-G-T		not specified	Uncertain significance (Jul 14, 2023)
15-74854632-C-G		not specified	Uncertain significance (May 03, 2023)
15-74854648-T-A		not specified	Uncertain significance (Apr 05, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SCAMP2	protein_coding	protein_coding	ENST00000268099	9	29636

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.160	0.839	125732	0	13	125745	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.30	130	179	0.727	0.00000970	2124
Missense in Polyphen		34	54.736	0.62116		671
Synonymous	0.185	73	75.0	0.973	0.00000429	667
Loss of Function	3.00	5	19.2	0.261	9.93e-7	195

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000797	0.0000791
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000654	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Functions in post-Golgi recycling pathways. Acts as a recycling carrier to the cell surface.
• Pathway: Serotonin Transporter Activity;Monoamine Transport;Arf6 trafficking events (Consensus)

Recessive Scores

• pRec: 0.105

Intolerance Scores

• loftool: 0.272
• rvis_EVS: -0.07
• rvis_percentile_EVS: 48.35

Haploinsufficiency Scores

• pHI: 0.223
• hipred: Y
• hipred_score: 0.654
• ghis: 0.519

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.876

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Scamp2

Gene ontology

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