SCAMP5

protein-coding

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

Gene summary

Involved in positive regulation of cytokine production; regulation of vesicle-mediated transport; and response to endoplasmic reticulum stress. Located in Golgi apparatus; plasma membrane; and recycling endosome membrane. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_138967.4

Inheritance

AR, AD

ClinVar variants

P:1U:26B:5

Top phenotype

neurodevelopmental disorder

gnomAD constraint

pLI —, LoF o/e 0.17

Max pathogenic AF

—

Genomic locus

chr15:74,957,219-75,021,495

External References & Databases

Ensembl (ENSG00000198794)

Transcript & Mutation Effects

hg38 • Region Span ~64.3 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

epilepsyLIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0005027

Submitter: Ambry Genetics

complex neurodevelopmental disorderMODERATE

Inheritance Pattern: AD

Disease ID:MONDO:0100038

Submitter: Illumina

complex neurodevelopmental disorderLIMITED

Inheritance Pattern: AD

Disease ID:MONDO:0100038

Submitter: Ambry Genetics

neurodevelopmental disorderSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0700092

Submitter: PanelApp Australia

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SCAMP5 variants in ClinVar

8 Conditions Cataloged

Inborn genetic diseasesTotal: 16

not providedTotal: 15

Neurodevelopmental disorderTotal: 1

SCAMP5-related disorderTotal: 1

Macrocephaly-developmental delay syndromeTotal: 1

SCAMP5-related neurodevelopmental disorder with autistic features and seizuresTotal: 1

SCAMP5-related conditionTotal: 1

SCAMP5-related neurodevelopmental and movement disorderTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_138967.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar	1 clinvar	2
missense	1 clinvar		22 clinvar	3 clinvar		26
nonsense			1 clinvar			1
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	1	0	26	4	1	32

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 68 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_138967.4	RefSeq	NP_620417.1	6	MANE Select
ENST00000425597.8	Ensembl	ENSP00000406547.3	6	MANE Select
NM_001178111.2	RefSeq	NP_001171582.1	6	Standard
NM_001178112.2	RefSeq	NP_001171583.1	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

exocytosis
protein transport
response to endoplasmic reticulum stress
negative regulation of endocytosis
positive regulation of calcium ion-dependent exocytosis

Molecular Function

protein binding
protein-containing complex binding

Cellular Component

Golgi membrane
Golgi apparatus
plasma membrane
integral component of membrane
cell junction

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000361900
Coding exons: 6
Length: 64278
Individuals with no LoFs: 124623
Homozygous LoFs: 0
Heterozygous LoFs: 2
Defined: 124625
p: 0.00000802

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.05	75	144	0.520	0.00000842	1562
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000044	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.0000088	0.0000088	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.458

Gene Damage Prediction

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