NM_198576.4(AGRN):c.1979G>T (p.Arg660Leu) AND Inborn genetic diseases

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Mar 4, 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:: RCV002547509.2

Allele description [Variation Report for NM_198576.4(AGRN):c.1979G>T (p.Arg660Leu)]

NM_198576.4(AGRN):c.1979G>T (p.Arg660Leu)

Gene:

AGRN:agrin [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

1p36.33

Genomic location:

Preferred name:

NM_198576.4(AGRN):c.1979G>T (p.Arg660Leu)

HGVS:

NC_000001.11:g.1044003G>T
NG_016346.1:g.28881G>T
NM_001305275.2:c.1979G>T
NM_001364727.2:c.1664G>T
NM_198576.3:c.1979G>T
NM_198576.4:c.1979G>TMANE SELECT
NP_001292204.1:p.Arg660Leu
NP_001351656.1:p.Arg555Leu
NP_940978.2:p.Arg660Leu
LRG_198:g.28881G>T
NC_000001.10:g.979383G>T

Protein change:

R555L

Links:

dbSNP: rs370983524

NCBI 1000 Genomes Browser:

rs370983524

Molecular consequence:

NM_001305275.2:c.1979G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001364727.2:c.1664G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_198576.4:c.1979G>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

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

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003708833	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Uncertain significance (Mar 4, 2022)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003708833

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Uncertain significance
(Mar 4, 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, SCV003708833.2

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

Description

The c.1979G>T (p.R660L) alteration is located in exon 10 (coding exon 10) of the AGRN gene. This alteration results from a G to T substitution at nucleotide position 1979, causing the arginine (R) at amino acid position 660 to be replaced by a leucine (L). Based on data from gnomAD, the T allele has an overall frequency of 0.001% (3/237176) total alleles studied. The highest observed frequency was 0.003% (3/106828) of European (non-Finnish) alleles. This amino acid position is not well conserved in available vertebrate species. This alteration is predicted to be tolerated by in silico analysis. 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: Sep 29, 2024

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