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NM_138967.4(SCAMP5):c.538G>T (p.Gly180Trp) AND SCAMP5-related neurodevelopmental disorder with autistic features and seizures

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Jun 1, 2023
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV003389252.1

Allele description [Variation Report for NM_138967.4(SCAMP5):c.538G>T (p.Gly180Trp)]

NM_138967.4(SCAMP5):c.538G>T (p.Gly180Trp)

Gene:
SCAMP5:secretory carrier membrane protein 5 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
15q24.2
Genomic location:
Preferred name:
NM_138967.4(SCAMP5):c.538G>T (p.Gly180Trp)
HGVS:
  • NC_000015.10:g.75018813G>T
  • NM_001178111.2:c.538G>T
  • NM_001178112.2:c.538G>T
  • NM_138967.4:c.538G>TMANE SELECT
  • NP_001171582.1:p.Gly180Trp
  • NP_001171583.1:p.Gly180Trp
  • NP_620417.1:p.Gly180Trp
  • NC_000015.9:g.75311154G>T
  • NM_001178111.1:c.538G>T
  • NR_033660.2:n.540G>T
Protein change:
G180W; GLY180TRP
Links:
OMIM: 613766.0001; dbSNP: rs1184981709
NCBI 1000 Genomes Browser:
rs1184981709
Molecular consequence:
  • NM_001178111.2:c.538G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001178112.2:c.538G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_138967.4:c.538G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NR_033660.2:n.540G>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:
SCAMP5-related neurodevelopmental disorder with autistic features and seizures
Identifiers:

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004101306Illumina Laboratory Services, Illumina
criteria provided, single submitter

(ICSLVariantClassificationCriteria RUGD 01 April 2020)		Likely pathogenic
(Jun 1, 2023) 		unknownclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Citation Link

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Identification of an Identical de Novo SCAMP5 Missense Variant in Four Unrelated Patients With Seizures and Severe Neurodevelopmental Delay.

Jiao X, Morleo M, Nigro V, Torella A, D'Arrigo S, Ciaccio C, Pantaleoni C, Gong P, Grand K, Sanchez-Lara PA, Krier J, Fieg E, Stergachis A, Wang X, Yang Z.

Front Pharmacol. 2020;11:599191. doi: 10.3389/fphar.2020.599191.

PubMed [citation]
PMID:
33390987
PMCID:
PMC7775611

De novo SCAMP5 mutation causes a neurodevelopmental disorder with autistic features and seizures.

Hubert L, Cannata Serio M, Villoing-Gaudé L, Boddaert N, Kaminska A, Rio M, Lyonnet S, Munnich A, Poirier K, Simons M, Besmond C.

J Med Genet. 2020 Feb;57(2):138-144. doi: 10.1136/jmedgenet-2018-105927. Epub 2019 Aug 22.

PubMed [citation]
PMID:
31439720

Details of each submission

From Illumina Laboratory Services, Illumina, SCV004101306.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

The SCAMP5 c.538G>T (p.Gly180Trp) missense variant has been reported in a de novo state in six unrelated individuals with developmental delay, seizures, motor disorders, behavioral differences, and abnormalities on brain MRI (PMID: 31439720; 33390987). This variant is not observed in version 2.1.1 or version 3.1.2 of the Genome Aggregation Database. Functional studies of this variant conducted in a Drosophila knock-in model suggest it has a dominant-negative effect (PMID: 31439720). This variant has been classified as pathogenic or likely pathogenic by four submitters in ClinVar. Based on the available evidence, the c.538G>T (p.Gly180Trp) variant is classified as likely pathogenic for SCAMP5-related neurodevelopmental disorder with autistic features and seizures.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Apr 7, 2025