NM_203446.3(SYNJ1):c.409A>G (p.Ile137Val) AND multiple conditions

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: May 17, 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:: RCV002006991.7

Allele description [Variation Report for NM_203446.3(SYNJ1):c.409A>G (p.Ile137Val)]

NM_203446.3(SYNJ1):c.409A>G (p.Ile137Val)

Gene:

SYNJ1:synaptojanin 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

21q22.11

Genomic location:

Preferred name:

NM_203446.3(SYNJ1):c.409A>G (p.Ile137Val)

HGVS:

NC_000021.9:g.32699908T>C
NG_030017.2:g.33132A>G
NM_001160302.2:c.409A>G
NM_001160306.2:c.409A>G
NM_003895.4:c.526A>G
NM_203446.3:c.409A>GMANE SELECT
NP_001153774.1:p.Ile137Val
NP_001153774.1:p.Ile137Val
NP_001153778.1:p.Ile137Val
NP_003886.3:p.Ile176Val
NP_003886.3:p.Ile176Val
NP_982271.3:p.Ile137Val
NC_000021.8:g.34072218T>C
NG_030017.1:g.33134A>G
NM_001160302.1:c.409A>G
NM_003895.3:c.526A>G

Protein change:

I137V

Links:

dbSNP: rs780191673

NCBI 1000 Genomes Browser:

rs780191673

Molecular consequence:

NM_001160302.2:c.409A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001160306.2:c.409A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_003895.4:c.526A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_203446.3:c.409A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Early-onset Parkinson disease 20
Identifiers:: MONDO: MONDO:0014233; MedGen: C3809824; Orphanet: 391411; OMIM: 615530

Name:: Developmental and epileptic encephalopathy, 53
Synonyms:: Epileptic encephalopathy, early infantile, 53
Identifiers:: MONDO: MONDO:0033362; MedGen: C4479313; OMIM: 617389

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002293847	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (May 17, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002293847

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(May 17, 2022)

germline

clinical testing

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

Help

Summary from all submissions

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

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group, Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9..

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002293847.4

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

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The valine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. This variant has not been reported in the literature in individuals affected with SYNJ1-related conditions. This variant is present in population databases (rs780191673, gnomAD 0.02%). This sequence change replaces isoleucine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 176 of the SYNJ1 protein (p.Ile176Val).

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

Last Updated: Mar 5, 2025

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