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NM_198576.4(AGRN):c.1978C>T (p.Arg660Trp) AND not specified

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jan 19, 2024
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:
RCV003987935.1

Allele description [Variation Report for NM_198576.4(AGRN):c.1978C>T (p.Arg660Trp)]

NM_198576.4(AGRN):c.1978C>T (p.Arg660Trp)

Gene:
AGRN:agrin [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
1p36.33
Genomic location:
Preferred name:
NM_198576.4(AGRN):c.1978C>T (p.Arg660Trp)
HGVS:
  • NC_000001.11:g.1044002C>T
  • NG_016346.1:g.28880C>T
  • NM_001305275.2:c.1978C>T
  • NM_001364727.2:c.1663C>T
  • NM_198576.4:c.1978C>TMANE SELECT
  • NP_001292204.1:p.Arg660Trp
  • NP_001351656.1:p.Arg555Trp
  • NP_940978.2:p.Arg660Trp
  • LRG_198:g.28880C>T
  • NC_000001.10:g.979382C>T
Protein change:
R555W
Links:
dbSNP: rs534519250
NCBI 1000 Genomes Browser:
rs534519250
Molecular consequence:
  • NM_001305275.2:c.1978C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001364727.2:c.1663C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_198576.4:c.1978C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004803919Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)		Uncertain significance
(Jan 19, 2024) 		germlineclinical testing

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV004803919.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

Variant summary: AGRN c.1978C>T (p.Arg660Trp) results in a non-conservative amino acid change located in one of the Kazal repeat domains (IPR002350) 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 7.5e-06 in 1,600,508 control chromosomes (i.e. 12 carriers) in the gnomAD database (v4 dataset). To our knowledge, no occurrence of c.1978C>T in individuals affected with &phenotype& and no experimental evidence demonstrating its impact on protein function have been reported. ClinVar contains an entry for this variant (Variation ID: 1408541). Based on the evidence outlined above, the variant was classified as uncertain significance.

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

Last Updated: Sep 29, 2024