NM_130811.4(SNAP25):c.593G>C (p.Arg198Pro) AND SNAP25 related neurodevelopmental disorder

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Jan 3, 2022
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:: RCV001810043.2

Allele description [Variation Report for NM_130811.4(SNAP25):c.593G>C (p.Arg198Pro)]

NM_130811.4(SNAP25):c.593G>C (p.Arg198Pro)

Gene:

SNAP25:synaptosome associated protein 25 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

20p12.2

Genomic location:

Preferred name:

NM_130811.4(SNAP25):c.593G>C (p.Arg198Pro)

HGVS:

NC_000020.11:g.10306169G>C
NG_029626.1:g.92341G>C
NM_001322902.2:c.593G>C
NM_001322903.2:c.593G>C
NM_001322904.2:c.593G>C
NM_001322905.2:c.593G>C
NM_001322906.2:c.593G>C
NM_001322907.2:c.593G>C
NM_001322908.2:c.593G>C
NM_001322909.2:c.593G>C
NM_001322910.2:c.593G>C
NM_003081.5:c.593G>C
NM_130811.4:c.593G>CMANE SELECT
NP_001309831.1:p.Arg198Pro
NP_001309832.1:p.Arg198Pro
NP_001309833.1:p.Arg198Pro
NP_001309834.1:p.Arg198Pro
NP_001309835.1:p.Arg198Pro
NP_001309836.1:p.Arg198Pro
NP_001309837.1:p.Arg198Pro
NP_001309838.1:p.Arg198Pro
NP_001309839.1:p.Arg198Pro
NP_003072.2:p.Arg198Pro
NP_570824.1:p.Arg198Pro
NC_000020.10:g.10286817G>C
NM_130811.3:c.593G>C

Protein change:

R198P

Links:

dbSNP: rs2064355563

NCBI 1000 Genomes Browser:

rs2064355563

Molecular consequence:

NM_001322902.2:c.593G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001322903.2:c.593G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001322904.2:c.593G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001322905.2:c.593G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001322906.2:c.593G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001322907.2:c.593G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001322908.2:c.593G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001322909.2:c.593G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001322910.2:c.593G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_003081.5:c.593G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_130811.4:c.593G>C - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Name:: SNAP25 related neurodevelopmental disorder
Identifiers:

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002058150	3billion	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Jan 3, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID] PMID:33299146

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002058150

3billion

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Jan 3, 2022)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

PMID:33299146

Help

Summary from all submissions

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

Citations

PubMed

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, SCV002058150.1

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

Description

Same nucleotide change resulting in same amino acid change has been previously reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV001066155, PS1_S). The variant has been previously reported as de novo in a similarly affected individual (PMID: 33299146, PS2_S). A missense variant is a common mechanism associated with SNAP25-related developmental delays and epileptic encephalopathies (PP2_P). It is not observed in the gnomAD v2.1.1 dataset (PM2_M). 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	germline	yes	1	not provided	not provided		1	not provided	not provided	not provided

Last Updated: Sep 29, 2024

ClinVar

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