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NM_173728.4(ARHGEF15):c.232C>T (p.Pro78Ser) AND Early infantile epileptic encephalopathy with suppression bursts

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Feb 21, 2018
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:
RCV000699664.8

Allele description [Variation Report for NM_173728.4(ARHGEF15):c.232C>T (p.Pro78Ser)]

NM_173728.4(ARHGEF15):c.232C>T (p.Pro78Ser)

Gene:
ARHGEF15:Rho guanine nucleotide exchange factor 15 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
17p13.1
Genomic location:
Preferred name:
NM_173728.4(ARHGEF15):c.232C>T (p.Pro78Ser)
HGVS:
  • NC_000017.11:g.8312271C>T
  • NG_034063.1:g.7034C>T
  • NM_025014.2:c.232C>T
  • NM_173728.4:c.232C>TMANE SELECT
  • NP_079290.1:p.Pro78Ser
  • NP_776089.2:p.Pro78Ser
  • NC_000017.10:g.8215589C>T
  • NM_173728.3:c.232C>T
Protein change:
P78S
Links:
dbSNP: rs1200503544
NCBI 1000 Genomes Browser:
rs1200503544
Molecular consequence:
  • NM_025014.2:c.232C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_173728.4:c.232C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Early infantile epileptic encephalopathy with suppression bursts (EIEE)
Synonyms:
Early infantile epileptic encephalopathy; Ohtahara syndrome; Developmental and epileptic encephalopathy
Identifiers:
MONDO: MONDO:0100062; MedGen: C0393706; Orphanet: 1934; OMIM: PS308350

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000828386Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Feb 21, 2018) 		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, SCV000828386.4

#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. Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The serine 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. This variant has not been reported in the literature in individuals with ARHGEF15-related disease. This variant is not present in population databases (ExAC no frequency). This sequence change replaces proline with serine at codon 78 of the ARHGEF15 protein (p.Pro78Ser). The proline residue is moderately conserved and there is a moderate physicochemical difference between proline and serine.

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

Last Updated: Sep 29, 2024