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NM_178565.5(RSPO2):c.125del (p.Gly42fs) AND Tetraamelia syndrome 2

Germline classification:
Likely pathogenic (2 submissions)
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:
RCV000656658.3

Allele description [Variation Report for NM_178565.5(RSPO2):c.125del (p.Gly42fs)]

NM_178565.5(RSPO2):c.125del (p.Gly42fs)

Gene:
RSPO2:R-spondin 2 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
8q23.1
Genomic location:
Preferred name:
NM_178565.5(RSPO2):c.125del (p.Gly42fs)
HGVS:
  • NC_000008.11:g.107989216del
  • NG_065170.1:g.99472del
  • NM_001282863.2:c.95-28397del
  • NM_001317942.2:c.-77del
  • NM_178565.5:c.125delMANE SELECT
  • NP_848660.3:p.Gly42fs
  • LRG_1405t1:c.125del
  • LRG_1405:g.99472del
  • LRG_1405p1:p.Gly42fs
  • NC_000008.10:g.109001444del
  • NM_178565.4:c.125del
  • NM_178565.5:c.125delGMANE SELECT
Protein change:
G42fs
Links:
OMIM: 610575.0001; dbSNP: rs1554579568
NCBI 1000 Genomes Browser:
rs1554579568
Molecular consequence:
  • NM_001317942.2:c.-77del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_178565.5:c.125del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001282863.2:c.95-28397del - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:
Tetraamelia syndrome 2
Synonyms:
TETRAAMELIA SYNDROME 2 WITH PULMONARY AGENESIS
Identifiers:
MONDO: MONDO:0060732; MedGen: C4747923; OMIM: 618021

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000778800OMIM
no assertion criteria provided
Pathogenic
(Jun 22, 2018) 		germlineliterature only

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

SCV002053999Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely pathogenicinheritedclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only
not providedinheritedyesnot providednot providednot provided3not providedclinical testing

Citations

PubMed

RSPO2 inhibition of RNF43 and ZNRF3 governs limb development independently of LGR4/5/6.

Szenker-Ravi E, Altunoglu U, Leushacke M, Bosso-Lefèvre C, Khatoo M, Thi Tran H, Naert T, Noelanders R, Hajamohideen A, Beneteau C, de Sousa SB, Karaman B, Latypova X, Başaran S, Yücel EB, Tan TT, Vlaminck L, Nayak SS, Shukla A, Girisha KM, Le Caignec C, Soshnikova N, et al.

Nature. 2018 May;557(7706):564-569. doi: 10.1038/s41586-018-0118-y. Epub 2018 May 16. Erratum in: Nature. 2018 Sep;561(7722):E7. doi: 10.1038/s41586-018-0296-7.

PubMed [citation]
PMID:
29769720

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 OMIM, SCV000778800.1

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

Description

In 3 affected fetuses with tetraamelia and pulmonary agenesis (TETAMS2; 618021) from a consanguineous Indian family (family 5), Szenker-Ravi et al. (2018) identified homozygosity for a 1-bp deletion (c.123delG, NM_178565) in exon 3 of the RSPO2 gene, causing a frameshift predicted to result in a premature termination codon (Gly42ValfsTer49) within the Furin-like 1 domain. The unaffected parents were each heterozygous for the mutation.

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

From Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India, SCV002053999.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1inheritedyes3not providednot providednot providednot providednot providednot provided

Last Updated: Feb 25, 2023