NM_016648.4(LARP7):c.627dup (p.Pro210fs) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Dec 25, 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:: RCV003689180.2

Allele description [Variation Report for NM_016648.4(LARP7):c.627dup (p.Pro210fs)]

NM_016648.4(LARP7):c.627dup (p.Pro210fs)

Genes:

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

Variant type:

Duplication

Cytogenetic location:

4q25

Genomic location:

Preferred name:

NM_016648.4(LARP7):c.627dup (p.Pro210fs)

HGVS:

NC_000004.12:g.112647108dup
NG_032779.1:g.15145dup
NM_001267039.4:c.627dup
NM_001370974.1:c.627dup
NM_001370975.1:c.627dup
NM_001370976.1:c.627dup
NM_001370977.1:c.627dup
NM_001370978.1:c.627dup
NM_001370979.1:c.627dup
NM_001370980.1:c.627dup
NM_001370981.1:c.390dup
NM_001370982.1:c.390dup
NM_015454.3:c.627dup
NM_016648.4:c.627dupMANE SELECT
NP_001253968.2:p.Pro210fs
NP_001357903.1:p.Pro210fs
NP_001357904.1:p.Pro210fs
NP_001357905.1:p.Pro210fs
NP_001357906.1:p.Pro210fs
NP_001357907.1:p.Pro210fs
NP_001357908.1:p.Pro210fs
NP_001357909.1:p.Pro210fs
NP_001357910.1:p.Pro131fs
NP_001357911.1:p.Pro131fs
NP_056269.1:p.Pro210fs
NP_057732.2:p.Pro210fs
NC_000004.11:g.113568262_113568263insT
NC_000004.11:g.113568264dup
NR_049768.1:n.802dup

Protein change:

P131fs

Molecular consequence:

NM_001267039.4:c.627dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001370974.1:c.627dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001370975.1:c.627dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001370976.1:c.627dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001370977.1:c.627dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001370978.1:c.627dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001370979.1:c.627dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001370980.1:c.627dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001370981.1:c.390dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001370982.1:c.390dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_015454.3:c.627dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_016648.4:c.627dup - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

Clear Turn Off Turn On

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
SCV004426718	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Dec 25, 2022)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 22865833, 26374271, 26607181, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004426718

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Dec 25, 2022)

germline

clinical testing

PubMed (4)
[See all records that cite these PMIDs]

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

Citations

PubMed

Loss of function mutation in LARP7, chaperone of 7SK ncRNA, causes a syndrome of facial dysmorphism, intellectual disability, and primordial dwarfism.

Alazami AM, Al-Owain M, Alzahrani F, Shuaib T, Al-Shamrani H, Al-Falki YH, Al-Qahtani SM, Alsheddi T, Colak D, Alkuraya FS.

Hum Mutat. 2012 Oct;33(10):1429-34. doi: 10.1002/humu.22175. Epub 2012 Aug 30.

PubMed [citation]

PMID:: 22865833

Compound heterozygous variants in the LARP7 gene as a cause of Alazami syndrome in a Caucasian female with significant failure to thrive, short stature, and developmental disability.

Ling TT, Sorrentino S.

Am J Med Genet A. 2016 Jan;170A(1):217-9. doi: 10.1002/ajmg.a.37396. Epub 2015 Sep 16.

PubMed [citation]

PMID:: 26374271

See all PubMed Citations (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004426718.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals affected with LARP7-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Pro210Serfs*41) in the LARP7 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in LARP7 are known to be pathogenic (PMID: 22865833, 26374271, 26607181).

#	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: Sep 29, 2024

ClinVar

Relating variation to medicine