U.S. flag

An official website of the United States government

NM_203446.3(SYNJ1):c.447G>T (p.Met149Ile) AND multiple conditions

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Apr 21, 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:
RCV001942401.7

Allele description [Variation Report for NM_203446.3(SYNJ1):c.447G>T (p.Met149Ile)]

NM_203446.3(SYNJ1):c.447G>T (p.Met149Ile)

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.447G>T (p.Met149Ile)
HGVS:
  • NC_000021.9:g.32699870C>A
  • NG_030017.2:g.33170G>T
  • NM_001160302.2:c.447G>T
  • NM_001160306.2:c.447G>T
  • NM_003895.4:c.564G>T
  • NM_203446.3:c.447G>TMANE SELECT
  • NP_001153774.1:p.Met149Ile
  • NP_001153774.1:p.Met149Ile
  • NP_001153778.1:p.Met149Ile
  • NP_003886.3:p.Met188Ile
  • NP_003886.3:p.Met188Ile
  • NP_982271.3:p.Met149Ile
  • NC_000021.8:g.34072180C>A
  • NG_030017.1:g.33172G>T
  • NM_001160302.1:c.447G>T
  • NM_003895.3:c.564G>T
Protein change:
M149I
Links:
dbSNP: rs2146212303
NCBI 1000 Genomes Browser:
rs2146212303
Molecular consequence:
  • NM_001160302.2:c.447G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001160306.2:c.447G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_003895.4:c.564G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_203446.3:c.447G>T - 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

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...

Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002134103Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Apr 21, 2021) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical 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, SCV002134103.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical 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. This sequence change replaces methionine with isoleucine at codon 188 of the SYNJ1 protein (p.Met188Ile). The methionine residue is moderately conserved and there is a small physicochemical difference between methionine and isoleucine. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals with SYNJ1-related conditions. 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 isoleucine amino acid residue is found in multiple mammalian species, suggesting that this missense change does not adversely affect protein function. These predictions have not been confirmed by published functional studies and their clinical significance is uncertain.

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

Last Updated: Mar 5, 2025