NM_016648.4(LARP7):c.618_619insTT (p.Lys207fs) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Feb 28, 2018
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:: RCV000627454.2

Allele description [Variation Report for NM_016648.4(LARP7):c.618_619insTT (p.Lys207fs)]

NM_016648.4(LARP7):c.618_619insTT (p.Lys207fs)

Genes:

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

Variant type:

Insertion

Cytogenetic location:

4q25

Genomic location:

Preferred name:

NM_016648.4(LARP7):c.618_619insTT (p.Lys207fs)

HGVS:

NC_000004.12:g.112647099_112647100insTT
NG_032779.1:g.15136_15137insTT
NM_001267039.4:c.618_619insTT
NM_001370974.1:c.618_619insTT
NM_001370975.1:c.618_619insTT
NM_001370976.1:c.618_619insTT
NM_001370977.1:c.618_619insTT
NM_001370978.1:c.618_619insTT
NM_001370979.1:c.618_619insTT
NM_001370980.1:c.618_619insTT
NM_001370981.1:c.381_382insTT
NM_001370982.1:c.381_382insTT
NM_015454.3:c.618_619insTT
NM_016648.4:c.618_619insTTMANE SELECT
NP_001253968.2:p.Lys207fs
NP_001357903.1:p.Lys207fs
NP_001357904.1:p.Lys207fs
NP_001357905.1:p.Lys207fs
NP_001357906.1:p.Lys207fs
NP_001357907.1:p.Lys207fs
NP_001357908.1:p.Lys207fs
NP_001357909.1:p.Lys207fs
NP_001357910.1:p.Lys128fs
NP_001357911.1:p.Lys128fs
NP_056269.1:p.Lys207fs
NP_057732.2:p.Lys207fs
NC_000004.11:g.113568255_113568256insTT
NM_016648.3:c.618_619insTT

Protein change:

K128fs

Links:

dbSNP: rs1554011503

NCBI 1000 Genomes Browser:

rs1554011503

Molecular consequence:

NM_001267039.4:c.618_619insTT - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001370974.1:c.618_619insTT - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001370975.1:c.618_619insTT - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001370976.1:c.618_619insTT - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001370977.1:c.618_619insTT - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001370978.1:c.618_619insTT - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001370979.1:c.618_619insTT - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001370980.1:c.618_619insTT - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001370981.1:c.381_382insTT - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001370982.1:c.381_382insTT - frameshift variant - [Sequence Ontology: SO:0001589]
NM_015454.3:c.618_619insTT - frameshift variant - [Sequence Ontology: SO:0001589]
NM_016648.4:c.618_619insTT - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: CN517202

Recent activity

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Microbe sample from Brevibacillus brevis
Microbe sample from Brevibacillus brevis

biosample
probable Family 9 glycosyl hydrolase [Sporisorium reilianum SRZ2]
probable Family 9 glycosyl hydrolase [Sporisorium reilianum SRZ2]
gi|323508199|emb|CBQ68070.1|

Protein
Verrucomicrobia bacterium SCGC AC-312-P03
Verrucomicrobia bacterium SCGC AC-312-P03
Verrucomicrobia bacterium SCGC AC-312-P03 Genome sequencing

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000748454	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Pathogenic (Feb 28, 2018)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000748454

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Pathogenic
(Feb 28, 2018)

germline

clinical testing

Citation Link

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	clinical testing

Details of each submission

From GeneDx, SCV000748454.3

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

Description

The c.618_619insTT variant in the LARP7 gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. The c.618_619insTT variant causes a frameshift starting with codon Lysine 207, changes this amino acid to a Leucine residue, and creates a premature Stop codon at position 7 of the new reading frame, denoted p.Lys207LeufsX7. This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The c.618_619insTT variant is not observed in large population cohorts (Lek et al., 2016). We interpret c.618_619insTT as a pathogenic variant.

#	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: May 24, 2022

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