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NM_004130.4(GYG1):c.143+3G>C AND not provided

Germline classification:
Pathogenic (3 submissions)
Last evaluated:
Feb 5, 2024
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:
RCV000387284.20

Allele description [Variation Report for NM_004130.4(GYG1):c.143+3G>C]

NM_004130.4(GYG1):c.143+3G>C

Gene:
GYG1:glycogenin 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
3q24
Genomic location:
Preferred name:
NM_004130.4(GYG1):c.143+3G>C
HGVS:
  • NC_000003.12:g.148994280G>C
  • NG_027677.1:g.7873G>C
  • NM_001184720.2:c.143+3G>C
  • NM_001184721.2:c.143+3G>C
  • NM_004130.4:c.143+3G>CMANE SELECT
  • NC_000003.11:g.148712067G>C
  • NM_004130.3:c.143+3G>C
  • p.Asp3Glufs*4
Nucleotide change:
IVS2DS, G-C, +3
Links:
OMIM: 603942.0003; dbSNP: rs370652040
NCBI 1000 Genomes Browser:
rs370652040
Molecular consequence:
  • NM_001184720.2:c.143+3G>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001184721.2:c.143+3G>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_004130.4:c.143+3G>C - intron variant - [Sequence Ontology: SO:0001627]
Observations:
1

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000329983GeneDx
criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)
Pathogenic
(Feb 5, 2024)
germlineclinical testing

Citation Link,

SCV002024931Revvity Omics, Revvity
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Mar 15, 2022)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV002586000CeGaT Center for Human Genetics Tuebingen
criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)
Pathogenic
(Sep 1, 2022)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not providednot providednot providednot providedclinical testing
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From GeneDx, SCV000329983.6

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

Description

Published functional studies demonstrate that c.143+3 G>C results in abnormal splicing, leading to skipping of exon 2 (PMID: 25272951); This variant is associated with the following publications: (PMID: 27663060, 25272951, 27066558, 26652229, 26203156, 28256728, 29264399, 34426522, 31589614, 32905144)

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

From Revvity Omics, Revvity, SCV002024931.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From CeGaT Center for Human Genetics Tuebingen, SCV002586000.13

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided

Description

GYG1: PP1:Strong, PM2, PM3, PS3:Moderate

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided1not providednot providednot provided

Last Updated: Sep 29, 2024