NM_016648.4(LARP7):c.320C>T (p.Thr107Ile) AND not specified

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Jul 25, 2023
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000202866.3

Allele description [Variation Report for NM_016648.4(LARP7):c.320C>T (p.Thr107Ile)]

NM_016648.4(LARP7):c.320C>T (p.Thr107Ile)

Gene:

LARP7:La ribonucleoprotein 7, transcriptional regulator [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

4q25

Genomic location:

Preferred name:

NM_016648.4(LARP7):c.320C>T (p.Thr107Ile)

Other names:

p.Thr114Ile

HGVS:

NC_000004.12:g.112646604C>T
NG_032779.1:g.14641C>T
NM_001267039.4:c.320C>T
NM_001370974.1:c.320C>T
NM_001370975.1:c.320C>T
NM_001370976.1:c.320C>T
NM_001370977.1:c.320C>T
NM_001370978.1:c.320C>T
NM_001370979.1:c.320C>T
NM_001370980.1:c.320C>T
NM_001370981.1:c.83C>T
NM_001370982.1:c.83C>T
NM_015454.3:c.320C>T
NM_016648.4:c.320C>TMANE SELECT
NP_001253968.2:p.Thr107Ile
NP_001357903.1:p.Thr107Ile
NP_001357904.1:p.Thr107Ile
NP_001357905.1:p.Thr107Ile
NP_001357906.1:p.Thr107Ile
NP_001357907.1:p.Thr107Ile
NP_001357908.1:p.Thr107Ile
NP_001357909.1:p.Thr107Ile
NP_001357910.1:p.Thr28Ile
NP_001357911.1:p.Thr28Ile
NP_056269.1:p.Thr107Ile
NP_057732.2:p.Thr107Ile
NC_000004.11:g.113567760C>T
NM_001267039.1:c.341C>T
NM_015454.2:c.320C>T
NM_016648.3:c.320C>T

Protein change:

T107I

Links:

dbSNP: rs200393300

NCBI 1000 Genomes Browser:

rs200393300

Molecular consequence:

NM_001267039.4:c.320C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001370974.1:c.320C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001370975.1:c.320C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001370976.1:c.320C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001370977.1:c.320C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001370978.1:c.320C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001370979.1:c.320C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001370980.1:c.320C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001370981.1:c.83C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001370982.1:c.83C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_015454.3:c.320C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_016648.4:c.320C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000257861	Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia	criteria provided, single submitter (DGD Variant Analysis Guidelines)	Uncertain significance (Dec 31, 2014)	unknown	clinical testing	DGD_Variant_Analysis_Guidelines.docx, Citation Link,
SCV004029163	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Uncertain significance (Jul 25, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000257861

Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia

criteria provided, single submitter

(DGD Variant Analysis Guidelines)

Uncertain significance
(Dec 31, 2014)

unknown

clinical testing

DGD_Variant_Analysis_Guidelines.docx,

Citation Link,

SCV004029163

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Uncertain significance
(Jul 25, 2023)

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

Details of each submission

From Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia, SCV000257861.2

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

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV004029163.1

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

Description

Variant summary: LARP7 c.320C>T (p.Thr107Ile) results in a non-conservative amino acid change located in the La-type HTH domain (IPR006630) of the encoded protein sequence. Three of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 0.00032 in 233580 control chromosomes. This frequency does not allow for any conclusion about variant significance. To our knowledge, no occurrence of c.320C>T in individuals affected with Microcephalic Primordial Dwarfism, Alazami Type and no experimental evidence demonstrating its impact on protein function have been reported in the literature. Five submitters have cited clinical-significance assessments for this variant to ClinVar after 2014: four classified the variant as uncertain significance, and one classified the variant as likely pathogenic. Based on the evidence outlined above, the variant was classified as uncertain significance.

#	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: Oct 20, 2024

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