NM_139058.3(ARX):c.433G>T (p.Ala145Ser) AND Developmental and epileptic encephalopathy, 1

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Feb 9, 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:: RCV002254363.4

Allele description [Variation Report for NM_139058.3(ARX):c.433G>T (p.Ala145Ser)]

NM_139058.3(ARX):c.433G>T (p.Ala145Ser)

Genes:

LOC109610631:aristaless related homeobox polyalanine expansion region [Gene]
ARX:aristaless related homeobox [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

Xp21.3

Genomic location:

Preferred name:

NM_139058.3(ARX):c.433G>T (p.Ala145Ser)

HGVS:

NC_000023.11:g.25013562C>A
NG_008281.1:g.7387G>T
NG_052655.1:g.133C>A
NM_139058.3:c.433G>TMANE SELECT
NP_620689.1:p.Ala145Ser
NC_000023.10:g.25031679C>A

Protein change:

A145S

Links:

dbSNP: rs1438576250

NCBI 1000 Genomes Browser:

rs1438576250

Molecular consequence:

NM_139058.3:c.433G>T - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Name:: Developmental and epileptic encephalopathy, 1 (DEE1)
Synonyms:: INFANTILE SPASM SYNDROME, X-LINKED 1; X-linked infantile spasms; West's syndrome; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0010632; MedGen: C3463992; OMIM: 308350

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KCNH6 potassium voltage-gated channel subfamily H member 6 [Homo sapiens]
KCNH6 potassium voltage-gated channel subfamily H member 6 [Homo sapiens]
Gene ID:81033

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002525512	Diagnostics Services (NGS), CSIR - Centre For Cellular And Molecular Biology	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Feb 9, 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

SCV002525512

Diagnostics Services (NGS), CSIR - Centre For Cellular And Molecular Biology

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Feb 9, 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	yes	1	1	not provided	not provided	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 Diagnostics Services (NGS), CSIR - Centre For Cellular And Molecular Biology, SCV002525512.1

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

Description

The c.433G>T variant is not present in publicly available population databases like 1000 Genomes, Exome Variant Server (EVS), Exome Aggregation Consortium (ExAC), Genome Aggregation Database (gnomAD), dbSNP and Indian Exome Database. The variant is not present in our in-house exome database. The variant was not reported previously to ClinVar, Human Genome Mutation Database (HGMD) and/or OMIM databases in any affected individuals. Predictions from different in-silico pathogenicity prediction programs like SIFT, PolyPhen-2, MutationTaster2, CADD etc. are contradictory, however these predictions were not confirmed by any established functional studies.

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

Last Updated: Oct 8, 2024

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