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NM_001365715.1(LRCH3):c.734C>T (p.Thr245Met) AND not specified

Germline classification:
Likely benign (1 submission)
Last evaluated:
Dec 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:
RCV004410728.1

Allele description [Variation Report for NM_001365715.1(LRCH3):c.734C>T (p.Thr245Met)]

NM_001365715.1(LRCH3):c.734C>T (p.Thr245Met)

Gene:
LRCH3:leucine rich repeats and calponin homology domain containing 3 [Gene - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
3q29
Genomic location:
Preferred name:
NM_001365715.1(LRCH3):c.734C>T (p.Thr245Met)
HGVS:
  • NC_000003.12:g.197826971C>T
  • NM_001363887.1:c.734C>T
  • NM_001365715.1:c.734C>TMANE SELECT
  • NM_001365716.1:c.734C>T
  • NM_001365717.1:c.734C>T
  • NM_001365718.1:c.734C>T
  • NM_001365719.2:c.734C>T
  • NM_032773.4:c.734C>T
  • NP_001350816.1:p.Thr245Met
  • NP_001352644.1:p.Thr245Met
  • NP_001352645.1:p.Thr245Met
  • NP_001352646.1:p.Thr245Met
  • NP_001352647.1:p.Thr245Met
  • NP_001352648.1:p.Thr245Met
  • NP_116162.1:p.Thr245Met
  • NC_000003.11:g.197553842C>T
  • NM_032773.2:c.734C>T
  • NR_158582.1:n.759C>T
Protein change:
T245M
Molecular consequence:
  • NM_001363887.1:c.734C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001365715.1:c.734C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001365716.1:c.734C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001365717.1:c.734C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001365718.1:c.734C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001365719.2:c.734C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_032773.4:c.734C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NR_158582.1:n.759C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004897390Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Likely benign
(Dec 20, 2023) 		germlineclinical testing

Citation Link

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Summary from all submissions

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

Details of each submission

From Ambry Genetics, SCV004897390.1

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

Description

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

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

Last Updated: May 7, 2024