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NM_032444.4(SLX4):c.4648C>T (p.Arg1550Trp) AND not provided

Germline classification:
Benign/Likely benign (5 submissions)
Last evaluated:
Jul 1, 2024
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV000437114.19

Allele description [Variation Report for NM_032444.4(SLX4):c.4648C>T (p.Arg1550Trp)]

NM_032444.4(SLX4):c.4648C>T (p.Arg1550Trp)

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.4648C>T (p.Arg1550Trp)
HGVS:
  • NC_000016.10:g.3584860G>A
  • NG_028123.1:g.31725C>T
  • NM_032444.4:c.4648C>TMANE SELECT
  • NP_115820.2:p.Arg1550Trp
  • LRG_503t1:c.4648C>T
  • LRG_503:g.31725C>T
  • NC_000016.9:g.3634861G>A
  • NM_032444.2:c.4648C>T
  • Q8IY92:p.Arg1550Trp
Protein change:
R1550W
Links:
UniProtKB: Q8IY92#VAR_069014; dbSNP: rs77021998
NCBI 1000 Genomes Browser:
rs77021998
Molecular consequence:
  • NM_032444.4:c.4648C>T - missense variant - [Sequence Ontology: SO:0001583]
Observations:
17

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
SCV000511776Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely Benign
(Oct 10, 2016)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV001800025Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) - VKGL Data-share Consensus
no assertion criteria provided
Likely benigngermlineclinical testing

SCV001950779GeneDx
criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)
Benign
(Feb 27, 2020)
germlineclinical testing

Citation Link,

SCV001963852Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus

See additional submitters

no assertion criteria provided
Likely benigngermlineclinical testing

SCV004144891CeGaT Center for Human Genetics Tuebingen
criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)
Likely benign
(Jul 1, 2024)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot providednot providednot providednot providednot providednot providedclinical testing
not providedgermlineyes17not providednot providednot providednot providedclinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics, SCV000511776.1

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

Description

Converted during submission to Likely benign.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot providednot provided0.00197not providednot provided

From Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) - VKGL Data-share Consensus, SCV001800025.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From GeneDx, SCV001950779.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 23840564, 23211700, 27153395, 22383991, 22911665)

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

From Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus, SCV001963852.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From CeGaT Center for Human Genetics Tuebingen, SCV004144891.10

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided17not providednot providedclinical testingnot provided

Description

SLX4: BP4, BS2

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided17not providednot providednot provided

Last Updated: Oct 20, 2024