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NM_018676.4(THSD1):c.670C>T (p.Arg224Ter) AND Lymphatic malformation 13

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jun 3, 2015
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
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:
RCV003224868.1

Allele description [Variation Report for NM_018676.4(THSD1):c.670C>T (p.Arg224Ter)]

NM_018676.4(THSD1):c.670C>T (p.Arg224Ter)

Gene:
THSD1:thrombospondin type 1 domain containing 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
13q14.3
Genomic location:
Preferred name:
NM_018676.4(THSD1):c.670C>T (p.Arg224Ter)
Other names:
THSD1, ARG224TER (rs9536062)
HGVS:
  • NC_000013.11:g.52397583G>A
  • NG_047168.1:g.13912C>T
  • NM_018676.4:c.670C>TMANE SELECT
  • NM_199263.3:c.670C>T
  • NP_061146.1:p.Arg224Ter
  • NP_954872.1:p.Arg224Ter
  • NC_000013.10:g.52971718G>A
  • NM_018676.3:c.670C>T
Note:
NCBI staff reviewed the variant in Fig. 2 of the paper by Shamseldin et al., 2015 (PubMed 26036949) to establish the HGVS expression for this allele.
Protein change:
R224*; ARG224TER
Links:
OMIM: 616821.0003; dbSNP: rs9536062
NCBI 1000 Genomes Browser:
rs9536062
Molecular consequence:
  • NM_018676.4:c.670C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_199263.3:c.670C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:
Lymphatic malformation 13 (LMPHM13)
Synonyms:
HYDROPS FETALIS, NONIMMUNE, WITH CARDIAC DEFECTS AND HEMANGIOMAS
Identifiers:
MONDO: MONDO:0859379; MedGen: C5830279; OMIM: 620244

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003840941OMIM
no assertion criteria provided
Pathogenic
(Jun 3, 2015) 		germlineliterature only

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only

Citations

PubMed

Identification of embryonic lethal genes in humans by autozygosity mapping and exome sequencing in consanguineous families.

Shamseldin HE, Tulbah M, Kurdi W, Nemer M, Alsahan N, Al Mardawi E, Khalifa O, Hashem A, Kurdi A, Babay Z, Bubshait DK, Ibrahim N, Abdulwahab F, Rahbeeni Z, Hashem M, Alkuraya FS.

Genome Biol. 2015 Jun 3;16:116. doi: 10.1186/s13059-015-0681-6.

PubMed [citation]
PMID:
26036949
PMCID:
PMC4491988

Details of each submission

From OMIM, SCV003840941.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (1)

Description

In 2 children with nonimmune hydrops fetalis (LMPHM13; 620244) from a consanguineous family (14DG1738), Shamseldin et al. (2015) reported homozygosity for a G-to-A transition at nucleotide 670 (c.670G-A, NM_018676) in exon 3 of the THSD1 gene resulting in an arg-to-ter substitution at codon 224 (R224X). Shamseldin et al. (2015) reported that this variant was seen in ExAC in heterozygosity in 2 individuals with an allele frequency of 1.6 x 10(-5). The mutation was predicted to truncate more than 75% of the protein sequence.

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

Last Updated: Aug 4, 2024