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NM_016097.5(IER3IP1):c.188T>C (p.Met63Thr) AND Microcephaly, epilepsy, and diabetes syndrome

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Aug 18, 2019
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:
RCV001219792.6

Allele description

NM_016097.5(IER3IP1):c.188T>C (p.Met63Thr)

Gene:
IER3IP1:immediate early response 3 interacting protein 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
18q21.1
Genomic location:
Preferred name:
NM_016097.5(IER3IP1):c.188T>C (p.Met63Thr)
HGVS:
  • NC_000018.10:g.47157441A>G
  • NG_031925.1:g.23934T>C
  • NM_016097.5:c.188T>CMANE SELECT
  • NP_057181.1:p.Met63Thr
  • NC_000018.9:g.44683812A>G
  • NM_016097.4:c.188T>C
Protein change:
M63T
Links:
dbSNP: rs2063964837
NCBI 1000 Genomes Browser:
rs2063964837
Molecular consequence:
  • NM_016097.5:c.188T>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Microcephaly, epilepsy, and diabetes syndrome
Identifiers:
MONDO: MONDO:0100328; MedGen: C3280240; Orphanet: 306558; OMIM: PS614231

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001391748Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Aug 18, 2019) 		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 Invitae, SCV001391748.5

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

Description

Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). 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 variant has not been reported in the literature in individuals with IER3IP1-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change replaces methionine with threonine at codon 63 of the IER3IP1 protein (p.Met63Thr). The methionine residue is highly conserved and there is a moderate physicochemical difference between methionine and threonine.

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

Last Updated: Feb 28, 2024