NM_001170535.3(ATAD3A):c.736A>G (p.Lys246Glu) AND multiple conditions

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Dec 18, 2020
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:: RCV001281072.2

Allele description [Variation Report for NM_001170535.3(ATAD3A):c.736A>G (p.Lys246Glu)]

NM_001170535.3(ATAD3A):c.736A>G (p.Lys246Glu)

Gene:

ATAD3A:ATPase family AAA domain containing 3A [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

1p36.33

Genomic location:

Preferred name:

NM_001170535.3(ATAD3A):c.736A>G (p.Lys246Glu)

HGVS:

NC_000001.11:g.1520603A>G
NG_053035.1:g.13461A>G
NM_001170535.3:c.736A>GMANE SELECT
NM_001170536.3:c.499A>G
NM_018188.5:c.880A>G
NP_001164006.1:p.Lys246Glu
NP_001164007.1:p.Lys167Glu
NP_060658.3:p.Lys294Glu
NC_000001.10:g.1455983A>G
NM_001170535.2:c.736A>G

Protein change:

K167E

Links:

dbSNP: rs1641555589

NCBI 1000 Genomes Browser:

rs1641555589

Molecular consequence:

NM_001170535.3:c.736A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001170536.3:c.499A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_018188.5:c.880A>G - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Name:: Harel-Yoon syndrome (HAYOS)
Synonyms:: Optic atrophy-peripheral neuropathy-developmental delay syndrome
Identifiers:: MONDO: MONDO:0014958; MedGen: C4310677; OMIM: 617183

Name:: Pontocerebellar hypoplasia, hypotonia, and respiratory insufficiency syndrome, neonatal lethal
Synonyms:: PHRINL SYNDROME
Identifiers:: MONDO: MONDO:0032931; MedGen: C5394137; OMIM: 618810

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001451356	Institute of Human Genetics, University of Goettingen	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Dec 18, 2020)	de novo	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

SCV001451356

Institute of Human Genetics, University of Goettingen

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Dec 18, 2020)

de novo

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
Non-Finnish European	de novo	unknown	1	not provided	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 Institute of Human Genetics, University of Goettingen, SCV001451356.1

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

Description

The variant c.736A>G (p.(Lys246Glu)) in exon 7 of the ATAD3A-gene is not found in known databases (ExAC or gnomAD), it affects a moderately conserved nucleotide, a highly conserved amino acid and there is a small physicochemical difference between Lys and Glu. This variant has a pathogenic computational verdict based on in silico prediction programs. This variant was found to be de novo in our patient. ACMG criteria used for classification: PM2, PM6, PP3.

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

Last Updated: Aug 15, 2022

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