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NM_001174147.2(LMX1B):c.209del (p.Arg70fs) AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Aug 23, 2023
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:
RCV003563972.1

Allele description

NM_001174147.2(LMX1B):c.209del (p.Arg70fs)

Gene:
LMX1B:LIM homeobox transcription factor 1 beta [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
9q33.3
Genomic location:
Preferred name:
NM_001174147.2(LMX1B):c.209del (p.Arg70fs)
HGVS:
  • NC_000009.12:g.126615452del
  • NG_017039.1:g.6010del
  • NM_001174146.2:c.209del
  • NM_001174147.2:c.209delMANE SELECT
  • NM_002316.4:c.209del
  • NP_001167617.1:p.Arg70fs
  • NP_001167618.1:p.Arg70fs
  • NP_002307.2:p.Arg70fs
  • LRG_1014t1:c.209del
  • LRG_1014t2:c.209del
  • LRG_1014t3:c.209del
  • LRG_1014:g.6010del
  • LRG_1014p1:p.Arg70fs
  • LRG_1014p2:p.Arg70fs
  • LRG_1014p3:p.Arg70fs
  • NC_000009.11:g.129377731del
Protein change:
R70fs
Molecular consequence:
  • NM_001174146.2:c.209del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001174147.2:c.209del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_002316.4:c.209del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004315291Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Aug 23, 2023) 		germlineclinical testing

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

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

Citations

PubMed

Mutations in LMX1B cause abnormal skeletal patterning and renal dysplasia in nail patella syndrome.

Dreyer SD, Zhou G, Baldini A, Winterpacht A, Zabel B, Cole W, Johnson RL, Lee B.

Nat Genet. 1998 May;19(1):47-50.

PubMed [citation]
PMID:
9590287

The human LMX1B gene: transcription unit, promoter, and pathogenic mutations.

Dunston JA, Hamlington JD, Zaveri J, Sweeney E, Sibbring J, Tran C, Malbroux M, O'Neill JP, Mountford R, McIntosh I.

Genomics. 2004 Sep;84(3):565-76.

PubMed [citation]
PMID:
15498463
See all PubMed Citations (3)

Details of each submission

From Invitae, SCV004315291.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

This sequence change creates a premature translational stop signal (p.Arg70Glnfs*59) in the LMX1B gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in LMX1B are known to be pathogenic (PMID: 9590287, 15498463). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with LMX1B-related conditions. For these reasons, this variant has been classified as Pathogenic.

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

Last Updated: Feb 20, 2024