NM_005094.4(SLC27A4):c.1799_1800del (p.Glu600fs) AND Ichthyosis prematurity syndrome

Clinical significance:Pathogenic/Likely pathogenic (Last evaluated: Mar 25, 2020)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV000988259.2

Allele description [Variation Report for NM_005094.4(SLC27A4):c.1799_1800del (p.Glu600fs)]

NM_005094.4(SLC27A4):c.1799_1800del (p.Glu600fs)

Gene:
SLC27A4:solute carrier family 27 member 4 [Gene - OMIM - HGNC]
Variant type:
Microsatellite
Cytogenetic location:
9q34.11
Genomic location:
Preferred name:
NM_005094.4(SLC27A4):c.1799_1800del (p.Glu600fs)
HGVS:
  • NC_000009.12:g.128360356AG[1]
  • NC_000009.12:g.128360356_128360357AG[1]
  • NG_017057.1:g.24797AG[1]
  • NM_005094.4:c.1799_1800delMANE SELECT
  • NP_005085.2:p.Glu600fs
  • NC_000009.11:g.131122635AG[1]
  • NC_000009.11:g.131122635_131122636delAG
  • NM_005094.3:c.1799_1800del
Protein change:
E600fs
Links:
dbSNP: rs758657421
NCBI 1000 Genomes Browser:
rs758657421
Molecular consequence:
  • NM_005094.4:c.1799_1800del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:
Ichthyosis prematurity syndrome (IPS)
Synonyms:
Ichthyosis congenita IV
Identifiers:
MONDO: MONDO:0012089; MedGen: C1837610; Orphanet: 88621; OMIM: 608649

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001137913Mendelicscriteria provided, single submitter
Pathogenic
(May 28, 2019)
unknownclinical testing

Citation Link,

SCV001443697Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diegocriteria provided, single submitter
Likely pathogenic
(Mar 25, 2020)
germlineclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing
not providedgermlineyesnot providednot 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 Mendelics, SCV001137913.1

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

From Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego, SCV001443697.1

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

Description

This frameshifting variant in exon 13 of 13 introduces a premature stop codon and is therefore predicted to result in loss of normal protein function through either protein truncation or nonsense-mediated mRNA decay (NMD). This variant has not been reported or functionally characterized in the literature to our knowledge. It is present in the heterozygous state in the gnomAD population database at a frequency of 0.001% (3/251470) and thus is presumed to be rare. Based on the available evidence, the c.1799_1800del (p.Glu600AlafsTer7) variant is classified as Likely Pathogenic.

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

Last Updated: Oct 7, 2021

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