NM_016648.4(LARP7):c.649_651del (p.Glu217del) AND not provided

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Dec 7, 2023
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:: RCV003717593.3

Allele description [Variation Report for NM_016648.4(LARP7):c.649_651del (p.Glu217del)]

NM_016648.4(LARP7):c.649_651del (p.Glu217del)

Genes:

LARP7:La ribonucleoprotein 7, transcriptional regulator [Gene - OMIM - HGNC]
MIR302CHG:miR-302/367 cluster host gene [Gene - HGNC]

Variant type:

Deletion

Cytogenetic location:

4q25

Genomic location:

Preferred name:

NM_016648.4(LARP7):c.649_651del (p.Glu217del)

HGVS:

NC_000004.12:g.112647201_112647203del
NG_032779.1:g.15238_15240del
NM_001267039.4:c.649_651del
NM_001370974.1:c.649_651del
NM_001370975.1:c.649_651del
NM_001370976.1:c.647-1_648del
NM_001370977.1:c.647-1_648del
NM_001370978.1:c.649_651del
NM_001370979.1:c.647-1_648del
NM_001370980.1:c.647-1_648del
NM_001370981.1:c.412_414del
NM_001370982.1:c.412_414del
NM_015454.3:c.649_651del
NM_016648.4:c.649_651delMANE SELECT
NP_001253968.2:p.Glu217del
NP_001357903.1:p.Glu217del
NP_001357904.1:p.Glu217del
NP_001357907.1:p.Glu217del
NP_001357910.1:p.Glu138del
NP_001357911.1:p.Glu138del
NP_056269.1:p.Glu217del
NP_057732.2:p.Glu217del
NC_000004.11:g.113568357_113568359del
NR_049768.1:n.824_826delGAG

Protein change:

E138del

Molecular consequence:

NM_001267039.4:c.649_651del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001370974.1:c.649_651del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001370975.1:c.649_651del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001370978.1:c.649_651del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001370981.1:c.412_414del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001370982.1:c.412_414del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_015454.3:c.649_651del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_016648.4:c.649_651del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001370976.1:c.647-1_648del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001370977.1:c.647-1_648del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001370979.1:c.647-1_648del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001370980.1:c.647-1_648del - splice acceptor variant - [Sequence Ontology: SO:0001574]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

Clear Turn Off Turn On

Chain A, Rho guanine nucleotide exchange factor 11
Chain A, Rho guanine nucleotide exchange factor 11
gi|159164200|pdb|2DLS|A

Protein

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004514490	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Dec 7, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV005190231	Breakthrough Genomics, Breakthrough Genomics	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance	germline	not provided	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004514490

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Dec 7, 2023)

germline

clinical testing

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

SCV005190231

Breakthrough Genomics, Breakthrough Genomics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance

germline

not provided

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

Help

Summary from all submissions

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

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

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 Labcorp Genetics (formerly Invitae), Labcorp, SCV004514490.1

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

Description

This variant, c.649_651del, results in the deletion of 1 amino acid(s) of the LARP7 protein (p.Glu217del), but otherwise preserves the integrity of the reading frame. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This variant has not been reported in the literature in individuals affected with LARP7-related conditions. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#	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

From Breakthrough Genomics, Breakthrough Genomics, SCV005190231.1

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

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

Last Updated: Sep 29, 2024

ClinVar

Relating variation to medicine