NM_145178.4(ATOH7):c.53del (p.Pro18fs) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 20, 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:: RCV001364298.7

Allele description [Variation Report for NM_145178.4(ATOH7):c.53del (p.Pro18fs)]

NM_145178.4(ATOH7):c.53del (p.Pro18fs)

Genes:

LOC130003943:ATAC-STARR-seq lymphoblastoid silent region 2418 [Gene]
ATOH7:atonal bHLH transcription factor 7 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

10q21.3

Genomic location:

Preferred name:

NM_145178.4(ATOH7):c.53del (p.Pro18fs)

HGVS:

NC_000010.11:g.68231629del
NG_031934.1:g.5489del
NM_145178.4:c.53delMANE SELECT
NP_660161.1:p.Pro18fs
NC_000010.10:g.69991382del
NC_000010.10:g.69991386del
NM_145178.3:c.53del

Protein change:

P18fs

Links:

OMIM: 609875.0003; dbSNP: rs587777665

NCBI 1000 Genomes Browser:

rs587777665

Molecular consequence:

NM_145178.4:c.53del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001560438	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Aug 20, 2022)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 22068589, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001560438

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Aug 20, 2022)

germline

clinical testing

PubMed (2)
[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

Next generation sequencing identifies mutations in Atonal homolog 7 (ATOH7) in families with global eye developmental defects.

Khan K, Logan CV, McKibbin M, Sheridan E, Elçioglu NH, Yenice O, Parry DA, Fernandez-Fuentes N, Abdelhamed ZI, Al-Maskari A, Poulter JA, Mohamed MD, Carr IM, Morgan JE, Jafri H, Raashid Y, Taylor GR, Johnson CA, Inglehearn CF, Toomes C, Ali M.

Hum Mol Genet. 2012 Feb 15;21(4):776-83. doi: 10.1093/hmg/ddr509. Epub 2011 Nov 7.

PubMed [citation]

PMID:: 22068589
PMCID:: PMC3263993

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, SCV001560438.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

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. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. ClinVar contains an entry for this variant (Variation ID: 144066). This premature translational stop signal has been observed in individual(s) with clinical features of persistent hyperplasia of the primary vitreous (PMID: 22068589). It has also been observed to segregate with disease in related individuals. This variant is present in population databases (rs587777665, gnomAD 0.006%). This sequence change creates a premature translational stop signal (p.Pro18Argfs*69) in the ATOH7 gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 135 amino acid(s) of the ATOH7 protein.

#	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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