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NM_032444.4(SLX4):c.3019C>A (p.Gln1007Lys) AND Fanconi anemia

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Dec 31, 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:
RCV001038907.13

Allele description [Variation Report for NM_032444.4(SLX4):c.3019C>A (p.Gln1007Lys)]

NM_032444.4(SLX4):c.3019C>A (p.Gln1007Lys)

Gene:
SLX4:SLX4 structure-specific endonuclease subunit [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
16p13.3
Genomic location:
Preferred name:
NM_032444.4(SLX4):c.3019C>A (p.Gln1007Lys)
HGVS:
  • NC_000016.10:g.3590619G>T
  • NG_028123.1:g.25966C>A
  • NM_032444.4:c.3019C>AMANE SELECT
  • NP_115820.2:p.Gln1007Lys
  • LRG_503t1:c.3019C>A
  • LRG_503:g.25966C>A
  • NC_000016.9:g.3640620G>T
  • NM_032444.2:c.3019C>A
Protein change:
Q1007K
Links:
dbSNP: rs138798067
NCBI 1000 Genomes Browser:
rs138798067
Molecular consequence:
  • NM_032444.4:c.3019C>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Fanconi anemia (FA)
Synonyms:
Fanconi pancytopenia; Fanconi's anemia
Identifiers:
MONDO: MONDO:0019391; MeSH: D005199; MedGen: C0015625; Orphanet: 84; OMIM: PS227650

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001202407Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Uncertain significance
(Dec 31, 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

Analysis of the novel fanconi anemia gene SLX4/FANCP in familial breast cancer cases.

Bakker JL, van Mil SE, Crossan G, Sabbaghian N, De Leeneer K, Poppe B, Adank M, Gille H, Verheul H, Meijers-Heijboer H, de Winter JP, Claes K, Tischkowitz M, Waisfisz Q.

Hum Mutat. 2013 Jan;34(1):70-3. doi: 10.1002/humu.22206. Epub 2012 Oct 11.

PubMed [citation]
PMID:
22911665

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, SCV001202407.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

This sequence change replaces glutamine, which is neutral and polar, with lysine, which is basic and polar, at codon 1007 of the SLX4 protein (p.Gln1007Lys). This variant is present in population databases (rs138798067, gnomAD 0.01%). This missense change has been observed in individual(s) with breast cancer (PMID: 22911665). ClinVar contains an entry for this variant (Variation ID: 837545). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be tolerated. 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.

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

Last Updated: Nov 3, 2024