NM_014319.5(LEMD3):c.1808_1812del (p.Thr603fs) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Feb 19, 2021
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:: RCV001869628.3

Allele description [Variation Report for NM_014319.5(LEMD3):c.1808_1812del (p.Thr603fs)]

NM_014319.5(LEMD3):c.1808_1812del (p.Thr603fs)

Gene:

LEMD3:LEM domain containing 3 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

12q14.3

Genomic location:

Preferred name:

NM_014319.5(LEMD3):c.1808_1812del (p.Thr603fs)

HGVS:

NC_000012.12:g.65238701_65238705del
NG_016210.2:g.74131_74135del
NM_001167614.2:c.1805_1809del
NM_014319.5:c.1808_1812delMANE SELECT
NP_001161086.1:p.Thr602fs
NP_055134.2:p.Thr603fs
NC_000012.11:g.65632481_65632485del

Protein change:

T602fs

Links:

dbSNP: rs2136353868

NCBI 1000 Genomes Browser:

rs2136353868

Molecular consequence:

NM_001167614.2:c.1805_1809del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_014319.5:c.1808_1812del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002198449	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Feb 19, 2021)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 15489854, 19438932, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002198449

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Feb 19, 2021)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Loss-of-function mutations in LEMD3 result in osteopoikilosis, Buschke-Ollendorff syndrome and melorheostosis.

Hellemans J, Preobrazhenska O, Willaert A, Debeer P, Verdonk PC, Costa T, Janssens K, Menten B, Van Roy N, Vermeulen SJ, Savarirayan R, Van Hul W, Vanhoenacker F, Huylebroeck D, De Paepe A, Naeyaert JM, Vandesompele J, Speleman F, Verschueren K, Coucke PJ, Mortier GR.

Nat Genet. 2004 Nov;36(11):1213-8. Epub 2004 Oct 17.

PubMed [citation]

PMID:: 15489854

Novel and recurrent germline LEMD3 mutations causing Buschke-Ollendorff syndrome and osteopoikilosis but not isolated melorheostosis.

Zhang Y, Castori M, Ferranti G, Paradisi M, Wordsworth BP.

Clin Genet. 2009 Jun;75(6):556-61. doi: 10.1111/j.1399-0004.2009.01177.x. Epub 2009 May 5. Erratum in: Clin Genet. 2011 Apr;79(4):401.

PubMed [citation]

PMID:: 19438932

See all PubMed Citations (3)

Details of each submission

From Invitae, SCV002198449.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals with LEMD3-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change creates a premature translational stop signal (p.Thr603Asnfs*3) in the LEMD3 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in LEMD3 are known to be pathogenic (PMID: 15489854, 19438932).

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Feb 28, 2024

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