NM_016648.4(LARP7):c.657_659del (p.Lys225del) AND Inborn genetic diseases

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 11, 2022
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:: RCV002699698.2

Allele description [Variation Report for NM_016648.4(LARP7):c.657_659del (p.Lys225del)]

NM_016648.4(LARP7):c.657_659del (p.Lys225del)

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.657_659del (p.Lys225del)

HGVS:

NC_000004.12:g.112647209_112647211del
NG_032779.1:g.15246_15248del
NM_001267039.4:c.657_659del
NM_001370974.1:c.657_659del
NM_001370975.1:c.657_659del
NM_001370976.1:c.654_656del
NM_001370977.1:c.654_656del
NM_001370978.1:c.657_659del
NM_001370979.1:c.654_656del
NM_001370980.1:c.654_656del
NM_001370981.1:c.420_422del
NM_001370982.1:c.420_422del
NM_015454.3:c.657_659del
NM_016648.4:c.657_659delMANE SELECT
NP_001253968.2:p.Lys225del
NP_001357903.1:p.Lys225del
NP_001357904.1:p.Lys225del
NP_001357905.1:p.Lys224del
NP_001357906.1:p.Lys224del
NP_001357907.1:p.Lys225del
NP_001357908.1:p.Lys224del
NP_001357909.1:p.Lys224del
NP_001357910.1:p.Lys146del
NP_001357911.1:p.Lys146del
NP_056269.1:p.Lys225del
NP_057732.2:p.Lys225del
NC_000004.11:g.113568365_113568367del
NM_016648.2:c.657_659delAAA
NR_049768.1:n.832_834delAAA

Protein change:

K146del

Molecular consequence:

NM_001267039.4:c.657_659del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001370974.1:c.657_659del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001370975.1:c.657_659del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001370976.1:c.654_656del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001370977.1:c.654_656del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001370978.1:c.657_659del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001370979.1:c.654_656del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001370980.1:c.654_656del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001370981.1:c.420_422del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001370982.1:c.420_422del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_015454.3:c.657_659del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_016648.4:c.657_659del - inframe_deletion - [Sequence Ontology: SO:0001822]

Condition(s)

Name:: Inborn genetic diseases
Identifiers:: MeSH: D030342; MedGen: C0950123

Recent activity

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D7Dcr22 AND (alive[prop]) (0)
Gene
phosphomannomutase CpsG [Serratia ureilytica]
phosphomannomutase CpsG [Serratia ureilytica]
gi|1998816800|gnl|PRJNA659846|J0X03 0|gb|QSR05913.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003744298	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Uncertain significance (Aug 11, 2022)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003744298

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Uncertain significance
(Aug 11, 2022)

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	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From Ambry Genetics, SCV003744298.2

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

Description

The c.657_659delAAA (p.K225del) alteration is located in exon 7 (coding exon 6) of the LARP7 gene. This alteration consists of an in-frame deletion of 3 nucleotides between nucleotide positions c.657 and c.659, resulting in the deletion of 1 residue. Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

#	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: May 1, 2024

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