NM_138967.4(SCAMP5):c.538G>T (p.Gly180Trp) AND Global developmental delay

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Oct 25, 2021
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:: RCV001779115.4

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]

Observations:

Condition(s)

Name:: Global developmental delay (DD)
Synonyms:: Cognitive delay
Identifiers:: MedGen: C0557874; Human Phenotype Ontology: HP:0001263

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002014729	3billion	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Oct 25, 2021)	unknown	clinical testing	PubMed (2) [See all records that cite these PMIDs] 31439720, 25741868

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002014729

3billion

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Oct 25, 2021)

unknown

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	unknown	yes	1	not provided	not provided	1	not provided	clinical testing

Citations

PubMed

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

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee.

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From 3billion, SCV002014729.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	not provided	clinical testing	PubMed (2)

Description

The variant has been previously reported as de novo insimilarly affected unrelated individual (PMID:31439720, PS2). It is not observed in the gnomAD v2.1.1 dataset (PM2). In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.649, 3Cnet: 0.848, PP3). Therefore, this variant is classified as likely pathogenic according to the recommendation of ACMG/AMP guideline.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	yes	1	not provided	not provided		1	not provided	not provided	not provided

Last Updated: Apr 20, 2025

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