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NM_016648.4(LARP7):c.461_462del (p.Ile154fs) AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Oct 16, 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:
RCV002706110.2

Allele description [Variation Report for NM_016648.4(LARP7):c.461_462del (p.Ile154fs)]

NM_016648.4(LARP7):c.461_462del (p.Ile154fs)

Genes:
LARP7:La ribonucleoprotein 7, transcriptional regulator [Gene - OMIM - HGNC]
MIR302CHG:miR-302/367 cluster host gene [Gene - HGNC]
Variant type:
Microsatellite
Cytogenetic location:
4q25
Genomic location:
Preferred name:
NM_016648.4(LARP7):c.461_462del (p.Ile154fs)
HGVS:
  • NC_000004.12:g.112646860TA[2]
  • NG_032779.1:g.14897TA[2]
  • NM_001267039.4:c.461_462del
  • NM_001370974.1:c.461_462del
  • NM_001370975.1:c.461_462del
  • NM_001370976.1:c.461_462del
  • NM_001370977.1:c.461_462del
  • NM_001370978.1:c.461_462del
  • NM_001370979.1:c.461_462del
  • NM_001370980.1:c.461_462del
  • NM_001370981.1:c.224_225del
  • NM_001370982.1:c.224_225del
  • NM_015454.3:c.461_462del
  • NM_016648.4:c.461_462delMANE SELECT
  • NP_001253968.2:p.Ile154fs
  • NP_001357903.1:p.Ile154fs
  • NP_001357904.1:p.Ile154fs
  • NP_001357905.1:p.Ile154fs
  • NP_001357906.1:p.Ile154fs
  • NP_001357907.1:p.Ile154fs
  • NP_001357908.1:p.Ile154fs
  • NP_001357909.1:p.Ile154fs
  • NP_001357910.1:p.Ile75fs
  • NP_001357911.1:p.Ile75fs
  • NP_056269.1:p.Ile154fs
  • NP_057732.2:p.Ile154fs
  • NC_000004.11:g.113568016TA[2]
  • NC_000004.11:g.113568016_113568017del
  • NR_049768.1:n.632_633TA[2]
  • NR_146092.1:n.251TA[2]
  • NR_146093.1:n.207TA[2]
  • NR_146094.1:n.154TA[2]
Protein change:
I154fs
Molecular consequence:
  • NM_001267039.4:c.461_462del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001370974.1:c.461_462del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001370975.1:c.461_462del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001370976.1:c.461_462del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001370977.1:c.461_462del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001370978.1:c.461_462del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001370979.1:c.461_462del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001370980.1:c.461_462del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001370981.1:c.224_225del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001370982.1:c.224_225del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_015454.3:c.461_462del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_016648.4:c.461_462del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NR_146092.1:n.251TA[2] - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_146093.1:n.207TA[2] - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_146094.1:n.154TA[2] - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

Recent activity

Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002996083Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Oct 16, 2022) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical 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, SCV002996083.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (4)

Description

This sequence change creates a premature translational stop signal (p.Ile154Lysfs*6) 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 present in population databases (no rsID available, gnomAD 0.003%). 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.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024