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NM_170707.4(LMNA):c.1718C>T (p.Ser573Leu) AND Familial partial lipodystrophy

Germline classification:
Benign (1 submission)
Last evaluated:
Jan 22, 2020
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:
RCV001248900.3

Allele description [Variation Report for NM_170707.4(LMNA):c.1718C>T (p.Ser573Leu)]

NM_170707.4(LMNA):c.1718C>T (p.Ser573Leu)

Gene:
LMNA:lamin A/C [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
1q22
Genomic location:
Preferred name:
NM_170707.4(LMNA):c.1718C>T (p.Ser573Leu)
Other names:
chr1-156138507-C-T
HGVS:
  • NC_000001.11:g.156138507C>T
  • NG_008692.2:g.60935C>T
  • NM_001257374.3:c.1382C>T
  • NM_001282626.2:c.1718C>T
  • NM_170707.4:c.1718C>TMANE SELECT
  • NM_170708.4:c.1628C>T
  • NP_001244303.1:p.Ser461Leu
  • NP_001269555.1:p.Ser573Leu
  • NP_733821.1:p.Ser573Leu
  • NP_733822.1:p.Ser543Leu
  • LRG_254t2:c.1718C>T
  • LRG_254:g.60935C>T
  • NC_000001.10:g.156108298C>T
  • NM_170707.2:c.1718C>T
  • NM_170707.3(LMNA):c.1718C>T
  • NM_170707.3:c.1718C>T
  • P02545:p.Ser573Leu
  • c.1718C>T
Protein change:
S461L; SER573LEU
Links:
UniProtKB: P02545#VAR_039789; OMIM: 150330.0041; dbSNP: rs60890628
NCBI 1000 Genomes Browser:
rs60890628
Molecular consequence:
  • NM_001257374.3:c.1382C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001282626.2:c.1718C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_170707.4:c.1718C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_170708.4:c.1628C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Familial partial lipodystrophy (FPLD)
Identifiers:
MONDO: MONDO:0020088; MedGen: C0271694; OMIM: PS151660

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001422587Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard
criteria provided, single submitter

(ACMG Guidelines, 2015)		Benign
(Jan 22, 2020) 		germlinecuration

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

Citation Link

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedcuration

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 Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard, SCV001422587.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcuration PubMed (1)

Description

The p.Ser573Leu variant in LMNA has been reported in 1 European individual with familial partial lipodystrophy (PMID: 17250669), but has been identified in 0.04% (4/10102) of Ashkenazi Jewish chromosomes and other populations at slightly lesser frequencies by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs60890628). This variant has been seen in the general population at a frequency high enough to rule out a pathogenic role. This variant has also been reported in ClinVar as having conflicting interpretations of pathogenicity (Variation ID: 14517). Computational prediction tools and conservation analyses do not provide strong support for or against an impact to the protein. In summary, this variant meets criteria to be classified as benign for familial partial lipodystrophy in an autosomal dominant manner based on its frequency in the general population. ACMG/AMP Criteria applied: BA1 (Richards 2015).

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

Last Updated: Oct 20, 2024