SCAMP4

protein-coding

secretory carrier membrane protein 4, the group of Secretory carrier membrane proteins

Gene summary

Secretory carrier membrane proteins (SCAMPs) are widely distributed integral membrane proteins implicated in membrane trafficking. Most SCAMPs (e.g., SCAMP1; MIM 606911) have N-terminal cytoplasmic NPF (arg-pro-phe) repeats, 4 central transmembrane regions, and a short C-terminal cytoplasmic tail. These SCAMPs likely have a role in endocytosis that is mediated by their NPF repeats. Other SCAMPs, such as SCAMP4, lack the NPF repeats and are therefore unlikely to function in endocytosis (summary by Fernandez-Chacon and Sudhof, 2000 [PubMed 11050114]).[supplied by OMIM, Feb 2011]

MANE transcript

NM_079834.4

Inheritance

—

ClinVar variants

U:61B:7

Top phenotype

Inborn genetic diseases

gnomAD constraint

pLI —, LoF o/e 0.44

Max pathogenic AF

—

Genomic locus

chr19:1,905,214-1,926,013

External References & Databases

Ensembl (ENSG00000227500)

Transcript & Mutation Effects

hg38 • Region Span ~20.8 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SCAMP4 variants in ClinVar

8 Conditions Cataloged

Inborn genetic diseasesTotal: 107

not specifiedTotal: 78

not providedTotal: 54

Intellectual disability-strabismus syndromeTotal: 30

ADAT3-related disorderTotal: 12

Intellectual disabilityTotal: 2

Neurodevelopmental disorder with brain abnormalitiesTotal: 1

MicrocephalyTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_079834.4. 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			4 clinvar	1 clinvar		5
missense			52 clinvar	6 clinvar		58
nonsense			2 clinvar			2
start loss			1 clinvar			1
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	61	7	0	68

Highest pathogenic variant AF is 0.0001902746

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 19 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_079834.4	RefSeq	NP_524558.1	6	MANE Select
ENST00000316097.13	Ensembl	ENSP00000316007.7	6	MANE Select
NM_001329539.2	RefSeq	NP_001316468.1	5	Standard
NM_001329540.2	RefSeq	NP_001316469.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

protein transport

Cellular Component

Golgi membrane
Golgi apparatus
integral component of membrane
trans-Golgi network membrane
recycling endosome membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000316097
Coding exons: 6
Length: 20804
Individuals with no LoFs: 124611
Homozygous LoFs: 0
Heterozygous LoFs: 18
Defined: 124629
p: 0.0000722

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.201	139	146	0.953	0.00000967	1477
Missense (PolyPhen)		52	58.832	0.88387		687
Synonymous	-1.19	80	67.6	1.18	0.00000532	432
Loss of Function	1.93	6	13.7	0.438	6.64e-7	131

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00026	0.00026	rare
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.00011	0.00011	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000082	0.000080	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Probably involved in membrane protein trafficking. {ECO:0000250}.;

Recessive Scores

pRec: 0.101

Intolerance Scores

LoFtool: 0.677
RVIS EVS: 0.22
RVIS percentile EVS: 68.27

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): E
Indispensability pred.: N
Indispensability score: 0.236

Gene Damage Prediction

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