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NM_181705.4(LYRM7):c.37del (p.Thr13fs) AND not provided

Germline classification:
Pathogenic (2 submissions)
Last evaluated:
Dec 16, 2018
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV000728000.5

Allele description [Variation Report for NM_181705.4(LYRM7):c.37del (p.Thr13fs)]

NM_181705.4(LYRM7):c.37del (p.Thr13fs)

Gene:
LYRM7:LYR motif containing 7 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
5q23.3
Genomic location:
Preferred name:
NM_181705.4(LYRM7):c.37del (p.Thr13fs)
HGVS:
  • NC_000005.10:g.131180113del
  • NG_034163.1:g.14200del
  • NM_001293735.2:c.37del
  • NM_181705.4:c.37delMANE SELECT
  • NP_001280664.1:p.Thr13fs
  • NP_859056.2:p.Thr13fs
  • NC_000005.9:g.130515806del
  • NM_181705.3:c.37delA
  • NR_121658.2:n.114del
Protein change:
T13fs
Links:
OMIM: 615831.0005; dbSNP: rs869025605
NCBI 1000 Genomes Browser:
rs869025605
Molecular consequence:
  • NM_001293735.2:c.37del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_181705.4:c.37del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NR_121658.2:n.114del - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000855518Eurofins Ntd Llc (ga)
criteria provided, single submitter

(EGL Classification Definitions 2015)
Pathogenic
(Jul 10, 2017)
germlineclinical testing

Citation Link,

SCV001168637GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))
Pathogenic
(Dec 16, 2018)
germlineclinical testing

Citation Link

Summary from all submissions

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

Details of each submission

From Eurofins Ntd Llc (ga), SCV000855518.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From GeneDx, SCV001168637.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The c.37delA variant has been published previously in a patient with leukoencephalopathy and mitochondrial complex III deficiency (Dallabona et al. 2016). The c.37delA variant is not observed in large population cohorts (Lek et al., 2016). The deletion causes a frameshift starting with codon Threonine 13, changes this amino acid to a Histidine residue and creates a premature Stop codon at position 17 of the new reading frame, denoted p.Thr13HisfsX17. This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. In summary, we interpret c.37delA as pathogenic.

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

Last Updated: Apr 1, 2023