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NM_005689.4(ABCB6):c.717G>A (p.Trp239Ter) AND not provided

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Mar 21, 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:
RCV003542272.1

Allele description [Variation Report for NM_005689.4(ABCB6):c.717G>A (p.Trp239Ter)]

NM_005689.4(ABCB6):c.717G>A (p.Trp239Ter)

Gene:
ABCB6:ATP binding cassette subfamily B member 6 (LAN blood group) [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
2q35
Genomic location:
Preferred name:
NM_005689.4(ABCB6):c.717G>A (p.Trp239Ter)
Other names:
Q239*
HGVS:
  • NC_000002.12:g.219216803C>T
  • NG_032110.1:g.7188G>A
  • NM_001349828.2:c.579G>A
  • NM_005689.4:c.717G>AMANE SELECT
  • NP_001336757.1:p.Trp193Ter
  • NP_005680.1:p.Trp239Ter
  • LRG_824t1:c.717G>A
  • LRG_824:g.7188G>A
  • LRG_824p1:p.Trp239Ter
  • NC_000002.11:g.220081525C>T
  • NM_005689.3:c.717G>A
Note:
ClinGen staff contributed the HGVS expression for this variant.
Protein change:
W193*; GLN239TER
Links:
OMIM: 605452.0001; dbSNP: rs148458820
NCBI 1000 Genomes Browser:
rs148458820
Molecular consequence:
  • NM_001349828.2:c.579G>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_005689.4:c.717G>A - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV004247294Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Uncertain significance
(Mar 21, 2023)
germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

ABCB6 is dispensable for erythropoiesis and specifies the new blood group system Langereis.

Helias V, Saison C, Ballif BA, Peyrard T, Takahashi J, Takahashi H, Tanaka M, Deybach JC, Puy H, Le Gall M, Sureau C, Pham BN, Le Pennec PY, Tani Y, Cartron JP, Arnaud L.

Nat Genet. 2012 Jan 15;44(2):170-3. doi: 10.1038/ng.1069.

PubMed [citation]
PMID:
22246506
PMCID:
PMC3664204

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 Invitae, SCV004247294.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical 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: 30477). This premature translational stop signal has been observed in individual(s) with blood group Langereis (PMID: 22246506). This variant is present in population databases (rs148458820, gnomAD 0.1%), and has an allele count higher than expected for a pathogenic variant. This sequence change creates a premature translational stop signal (p.Trp239*) in the ABCB6 gene. It is expected to result in an absent or disrupted protein product. However, the current clinical and genetic evidence is not sufficient to establish whether loss-of-function variants in ABCB6 cause disease.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Feb 20, 2024