NM_016648.4(LARP7):c.520G>T (p.Glu174Ter) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Oct 27, 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:: RCV003580172.2

Allele description [Variation Report for NM_016648.4(LARP7):c.520G>T (p.Glu174Ter)]

NM_016648.4(LARP7):c.520G>T (p.Glu174Ter)

Genes:

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

Variant type:

single nucleotide variant

Cytogenetic location:

4q25

Genomic location:

Preferred name:

NM_016648.4(LARP7):c.520G>T (p.Glu174Ter)

HGVS:

NC_000004.12:g.112646923G>T
NG_032779.1:g.14960G>T
NM_001267039.4:c.520G>T
NM_001370974.1:c.520G>T
NM_001370975.1:c.520G>T
NM_001370976.1:c.520G>T
NM_001370977.1:c.520G>T
NM_001370978.1:c.520G>T
NM_001370979.1:c.520G>T
NM_001370980.1:c.520G>T
NM_001370981.1:c.283G>T
NM_001370982.1:c.283G>T
NM_015454.3:c.520G>T
NM_016648.4:c.520G>TMANE SELECT
NP_001253968.2:p.Glu174Ter
NP_001357903.1:p.Glu174Ter
NP_001357904.1:p.Glu174Ter
NP_001357905.1:p.Glu174Ter
NP_001357906.1:p.Glu174Ter
NP_001357907.1:p.Glu174Ter
NP_001357908.1:p.Glu174Ter
NP_001357909.1:p.Glu174Ter
NP_001357910.1:p.Glu95Ter
NP_001357911.1:p.Glu95Ter
NP_056269.1:p.Glu174Ter
NP_057732.2:p.Glu174Ter
NC_000004.11:g.113568079G>T
NR_049768.1:n.695G>T
NR_146092.1:n.193C>A
NR_146093.1:n.149C>A
NR_146094.1:n.96C>A

Protein change:

E174*

Molecular consequence:

NR_146092.1:n.193C>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_146093.1:n.149C>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_146094.1:n.96C>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_001267039.4:c.520G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001370974.1:c.520G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001370975.1:c.520G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001370976.1:c.520G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001370977.1:c.520G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001370978.1:c.520G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001370979.1:c.520G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001370980.1:c.520G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001370981.1:c.283G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001370982.1:c.283G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_015454.3:c.520G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_016648.4:c.520G>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004333075	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Oct 27, 2023)	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

SCV004333075

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Oct 27, 2023)

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, SCV004333075.1

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

Description

This sequence change creates a premature translational stop signal (p.Glu174*) 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). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with LARP7-related conditions. For these reasons, this variant has been classified as Pathogenic.

#	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

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