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NM_001174147.2(LMX1B):c.175T>C (p.Cys59Arg) AND LMX1B-related disorder

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Oct 20, 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:
RCV003973630.1

Allele description

NM_001174147.2(LMX1B):c.175T>C (p.Cys59Arg)

Gene:
LMX1B:LIM homeobox transcription factor 1 beta [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
9q33.3
Genomic location:
Preferred name:
NM_001174147.2(LMX1B):c.175T>C (p.Cys59Arg)
HGVS:
  • NC_000009.12:g.126615418T>C
  • NG_017039.1:g.5976T>C
  • NM_001174146.2:c.175T>C
  • NM_001174147.2:c.175T>CMANE SELECT
  • NM_002316.3:c.175T>C
  • NM_002316.4:c.175T>C
  • NP_001167617.1:p.Cys59Arg
  • NP_001167618.1:p.Cys59Arg
  • NP_002307.2:p.Cys59Arg
  • LRG_1014t1:c.175T>C
  • LRG_1014t2:c.175T>C
  • LRG_1014t3:c.175T>C
  • LRG_1014:g.5976T>C
  • LRG_1014p1:p.Cys59Arg
  • LRG_1014p2:p.Cys59Arg
  • LRG_1014p3:p.Cys59Arg
  • NC_000009.11:g.129377697T>C
Protein change:
C59R
Molecular consequence:
  • NM_001174146.2:c.175T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001174147.2:c.175T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_002316.4:c.175T>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
LMX1B-related disorder
Synonyms:
LMX1B-related condition
Identifiers:

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004795807PreventionGenetics, part of Exact Sciences
criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely pathogenic
(Oct 20, 2023) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot 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 PreventionGenetics, part of Exact Sciences, SCV004795807.1

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

Description

The LMX1B c.175T>C variant is predicted to result in the amino acid substitution p.Cys59Arg. This variant was reported in an individual with nail-patella syndrome (Reported as 106T>C, C36R in Clough et al 1999. PubMed ID: 10571942). A different amino acid change at this position (p.Cys59Ser) has also been reported in an individual with nail-patella syndrome (Reported as 107G>C, C36S in Clough et al 1999. PubMed ID: 10571942). An outside lab has reported this variant as pathogenic in ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/variation/2136808/). This variant has not been reported in a large population database (http://gnomad.broadinstitute.org), indicating this variant is rare. This variant is interpreted as likely pathogenic.

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

Last Updated: Sep 29, 2024