SCAMP1

secretory carrier membrane protein 1, the group of Secretory carrier membrane proteins

Basic information

Region (hg38): 5:78360610-78480739

Links

ENSG00000085365 ∙ NCBI:9522 ∙ OMIM:606911 ∙ HGNC:10563 ∙ Uniprot:O15126 ∙ 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 SCAMP1 gene.

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			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
5-78416647-A-G		not specified	Uncertain significance (Jun 10, 2024)
5-78418852-A-G		not specified	Uncertain significance (May 18, 2023)
5-78421854-G-A		not specified	Uncertain significance (Aug 09, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SCAMP1	protein_coding	protein_coding	ENST00000538629	9	120224

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.977	0.0230	123037	0	1	123038	0.00000406

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.42	76	163	0.467	0.00000798	2202
Missense in Polyphen		21	59.037	0.35571		824
Synonymous	1.18	45	56.2	0.801	0.00000295	626
Loss of Function	3.47	1	16.0	0.0626	7.67e-7	206

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000895	0.00000895
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
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: 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

Essentials

• 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: 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