NM_000350.3(ABCA4):c.2032_2034del (p.Lys678del) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 4, 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:: RCV003030750.3

Allele description [Variation Report for NM_000350.3(ABCA4):c.2032_2034del (p.Lys678del)]

NM_000350.3(ABCA4):c.2032_2034del (p.Lys678del)

Gene:

ABCA4:ATP binding cassette subfamily A member 4 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

1p22.1

Genomic location:

Preferred name:

NM_000350.3(ABCA4):c.2032_2034del (p.Lys678del)

HGVS:

NC_000001.11:g.94060665_94060667del
NG_009073.2:g.65483_65485del
NM_000350.3:c.2032_2034delMANE SELECT
NM_001425324.1:c.2030_2032delAGA
NP_000341.2:p.Lys678del
NP_001412253.1:p.Lys678del
NC_000001.10:g.94526219_94526221del
NC_000001.10:g.94526221_94526223del
NG_009073.1:g.65485_65487del

Protein change:

K678del

Molecular consequence:

NM_000350.3:c.2032_2034del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001425324.1:c.2030_2032delAGA - inframe_indel - [Sequence Ontology: SO:0001820]

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
SCV003310470	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Aug 4, 2023)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 33301772, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003310470

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Aug 4, 2023)

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

Clinical and genetic analysis of the ABCA4 gene associated retinal dystrophy in a large Chinese cohort.

Sun Z, Yang L, Li H, Zou X, Wang L, Wu S, Zhu T, Wei X, Zhong Y, Sui R.

Exp Eye Res. 2021 Jan;202:108389. doi: 10.1016/j.exer.2020.108389. Epub 2020 Dec 7.

PubMed [citation]

PMID:: 33301772

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, SCV003310470.2

#	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. ClinVar contains an entry for this variant (Variation ID: 2098056). This variant has been observed in individual(s) with Stargardt disease (PMID: 33301772). This variant is not present in population databases (gnomAD no frequency). This variant, c.2032_2034del, results in the deletion of 1 amino acid(s) of the ABCA4 protein (p.Lys678del), but otherwise preserves the integrity of the reading frame.

#	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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