SCAMP5

secretory carrier membrane protein 5, the group of Secretory carrier membrane proteins

Basic information

Region (hg38): 15:74957219-75021495

Links

ENSG00000198794 ∙ NCBI:192683 ∙ OMIM:613766 ∙ HGNC:30386 ∙ Uniprot:Q8TAC9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• complex neurodevelopmental disorder (Limited), mode of inheritance: AD
• epilepsy (Limited), mode of inheritance: AR
• complex neurodevelopmental disorder (Moderate), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SCAMP5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SCAMP5 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					1	1
missense		1	8	2		11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	1	8	2	1

Variants in SCAMP5

This is a list of pathogenic ClinVar variants found in the SCAMP5 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-75012709-T-G			Uncertain significance (Nov 10, 2024)
15-75012717-G-T			Benign (Dec 31, 2019)
15-75012758-C-A			Uncertain significance (May 30, 2024)
15-75012806-G-A			Uncertain significance (Jun 12, 2024)
15-75016676-G-A		Inborn genetic diseases	Uncertain significance (Oct 05, 2022)
15-75016727-C-T		Inborn genetic diseases	Uncertain significance (Apr 07, 2022)
15-75016739-A-G		Inborn genetic diseases	Uncertain significance (May 11, 2022)
15-75017946-G-A		Inborn genetic diseases	Uncertain significance (Dec 08, 2023)
15-75018509-G-A		Inborn genetic diseases	Likely benign (Sep 16, 2021)
15-75018813-G-T		Global developmental delay • Inborn genetic diseases • SCAMP5-related neurodevelopmental disorder with autistic features and seizures • Macrocephaly-developmental delay syndrome	Pathogenic/Likely pathogenic (Nov 30, 2023)
15-75018840-G-A			Uncertain significance (Mar 04, 2024)
15-75018867-C-G		Inborn genetic diseases	Uncertain significance (Sep 29, 2023)
15-75018948-G-A		Inborn genetic diseases	Uncertain significance (Sep 30, 2022)
15-75018973-A-G		Inborn genetic diseases	Likely benign (Nov 05, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SCAMP5	protein_coding	protein_coding	ENST00000361900	6	64278

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.651	0.348	124623	0	2	124625	0.00000802

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.05	75	144	0.520	0.00000842	1562
Missense in Polyphen		28	64.964	0.43101		704
Synonymous	-0.864	68	59.5	1.14	0.00000429	439
Loss of Function	2.68	2	12.0	0.166	5.16e-7	123

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000435	0.0000435
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000885	0.00000885
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for the calcium-dependent exocytosis of signal sequence-containing cytokines such as CCL5. Probably acts in cooperation with the SNARE machinery. May play a role in accumulation of expanded polyglutamine (polyQ) protein huntingtin (HTT) in case of endoplasmic reticulum stress by inhibiting the endocytosis pathway. {ECO:0000269|PubMed:19234194}.

Recessive Scores

• pRec: 0.109

Intolerance Scores

• loftool: 0.563
• rvis_EVS: -0.34
• rvis_percentile_EVS: 30.07

Haploinsufficiency Scores

• pHI: 0.437
• hipred: Y
• hipred_score: 0.651
• ghis: 0.706

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.458

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Scamp5

Gene ontology

• Biological process: exocytosis;protein transport;response to endoplasmic reticulum stress;negative regulation of endocytosis;positive regulation of calcium ion-dependent exocytosis;positive regulation of cytokine secretion
• Cellular component: Golgi membrane;Golgi apparatus;plasma membrane;integral component of membrane;cell junction;synaptic vesicle membrane;trans-Golgi network membrane;recycling endosome membrane
• Molecular function: protein binding;protein-containing complex binding