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NM_001042545.2(LTBP4):c.688G>T (p.Glu230Ter) AND Cutis laxa with severe pulmonary, gastrointestinal and urinary anomalies

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Apr 20, 2022
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:
RCV002467376.3

Allele description [Variation Report for NM_001042545.2(LTBP4):c.688G>T (p.Glu230Ter)]

NM_001042545.2(LTBP4):c.688G>T (p.Glu230Ter)

Genes:
LOC130064475:ATAC-STARR-seq lymphoblastoid silent region 10639 [Gene]
LTBP4:latent transforming growth factor beta binding protein 4 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
19q13.2
Genomic location:
Preferred name:
NM_001042545.2(LTBP4):c.688G>T (p.Glu230Ter)
HGVS:
  • NC_000019.10:g.40605650G>T
  • NG_021201.1:g.17485G>T
  • NM_001042544.1:c.889G>T
  • NM_001042545.2:c.688G>TMANE SELECT
  • NM_003573.2:c.778G>T
  • NP_001036009.1:p.Glu297Ter
  • NP_001036010.1:p.Glu230Ter
  • NP_003564.2:p.Glu260Ter
  • NC_000019.9:g.41111556G>T
Protein change:
E230*
Molecular consequence:
  • NM_001042544.1:c.889G>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001042545.2:c.688G>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_003573.2:c.778G>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:
Cutis laxa with severe pulmonary, gastrointestinal and urinary anomalies
Synonyms:
URBAN-RIFKIN-DAVIS SYNDROME; Cutis laxa with severe pulmonary, gastrointestinal, and urinary abnormalities; Cutis laxa, autosomal recessive, type IC
Identifiers:
MONDO: MONDO:0013170; MedGen: C2750804; Orphanet: 221145; OMIM: 613177

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002762691Illumina Laboratory Services, Illumina
criteria provided, single submitter

(ICSLVariantClassificationCriteria RUGD 01 April 2020)		Pathogenic
(Apr 20, 2022) 		unknownclinical testing

Citation Link

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Summary from all submissions

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

Details of each submission

From Illumina Laboratory Services, Illumina, SCV002762691.1

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

Description

The LTBP4 c.688G>T (p.Glu230Ter) nonsense variant results in the substitution of glutamine at amino acid position 230 with a stop codon. Loss of normal protein function through either protein truncation or nonsense-mediated mRNA decay is expected. To our knowledge, this variant has not been reported in the peer-reviewed literature. This variant is not found in version 2.1.1 or version 3.1.2 of the Genome Aggregation Database. This variant was identified in a compound heterozygous state with a second loss-of-function variant. Based on the available evidence, the c.688G>T (p.Glu230Ter) variant is classified as pathogenic for cutis laxa with severe pulmonary, gastrointestinal, and urinary abnormalities.

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

Last Updated: Oct 14, 2023