NM_007348.4(ATF6):c.206G>A (p.Trp69Ter) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jun 9, 2023
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:: RCV003547335.2

Allele description [Variation Report for NM_007348.4(ATF6):c.206G>A (p.Trp69Ter)]

NM_007348.4(ATF6):c.206G>A (p.Trp69Ter)

Gene:

ATF6:activating transcription factor 6 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

1q23.3

Genomic location:

Preferred name:

NM_007348.4(ATF6):c.206G>A (p.Trp69Ter)

HGVS:

NC_000001.11:g.161781958G>A
NG_029773.1:g.20715G>A
NM_001410890.1:c.206G>A
NM_007348.4:c.206G>AMANE SELECT
NP_001397819.1:p.Trp69Ter
NP_031374.2:p.Trp69Ter
NC_000001.10:g.161751748G>A

Protein change:

W69*

Molecular consequence:

NM_001410890.1:c.206G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_007348.4:c.206G>A - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Lmnb2 lamin B2 [Rattus norvegicus]
Lmnb2 lamin B2 [Rattus norvegicus]
Gene ID:299625

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004251275	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jun 9, 2023)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 26029869, 26063662, 26070061, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004251275

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jun 9, 2023)

germline

clinical testing

PubMed (4)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Mutations in the unfolded protein response regulator ATF6 cause the cone dysfunction disorder achromatopsia.

Kohl S, Zobor D, Chiang WC, Weisschuh N, Staller J, Gonzalez Menendez I, Chang S, Beck SC, Garcia Garrido M, Sothilingam V, Seeliger MW, Stanzial F, Benedicenti F, Inzana F, Héon E, Vincent A, Beis J, Strom TM, Rudolph G, Roosing S, Hollander AI, Cremers FP, et al.

Nat Genet. 2015 Jul;47(7):757-65. doi: 10.1038/ng.3319. Epub 2015 Jun 1.

PubMed [citation]

PMID:: 26029869
PMCID:: PMC4610820

Mutation of ATF6 causes autosomal recessive achromatopsia.

Ansar M, Santos-Cortez RL, Saqib MA, Zulfiqar F, Lee K, Ashraf NM, Ullah E, Wang X, Sajid S, Khan FS, Amin-ud-Din M; University of Washington Center for Mendelian Genomics., Smith JD, Shendure J, Bamshad MJ, Nickerson DA, Hameed A, Riazuddin S, Ahmed ZM, Ahmad W, Leal SM.

Hum Genet. 2015 Sep;134(9):941-50. doi: 10.1007/s00439-015-1571-4. Epub 2015 Jun 11.

PubMed [citation]

PMID:: 26063662
PMCID:: PMC4529463

See all PubMed Citations (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004251275.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

For these reasons, this variant has been classified as Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. This variant has not been reported in the literature in individuals affected with ATF6-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Trp69*) in the ATF6 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in ATF6 are known to be pathogenic (PMID: 26029869, 26063662, 26070061).

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

Last Updated: Sep 29, 2024

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