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NM_006348.5(COG5):c.1756C>T (p.His586Tyr) AND not specified

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Sep 26, 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:
RCV004782451.1

Allele description [Variation Report for NM_006348.5(COG5):c.1756C>T (p.His586Tyr)]

NM_006348.5(COG5):c.1756C>T (p.His586Tyr)

Gene:
COG5:component of oligomeric golgi complex 5 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
7q22.3
Genomic location:
Preferred name:
NM_006348.5(COG5):c.1756C>T (p.His586Tyr)
HGVS:
  • NC_000007.14:g.107248493G>A
  • NG_028095.2:g.321022C>T
  • NM_001161520.2:c.1756C>T
  • NM_001379511.1:c.1594C>T
  • NM_001379512.1:c.1582C>T
  • NM_001379513.1:c.1756C>T
  • NM_001379514.1:c.1756C>T
  • NM_001379515.1:c.1186C>T
  • NM_001379516.1:c.1042C>T
  • NM_006348.5:c.1756C>TMANE SELECT
  • NM_181733.4:c.1693C>T
  • NP_001154992.2:p.His586Tyr
  • NP_001366440.1:p.His532Tyr
  • NP_001366441.1:p.His528Tyr
  • NP_001366442.1:p.His586Tyr
  • NP_001366443.1:p.His586Tyr
  • NP_001366444.1:p.His396Tyr
  • NP_001366445.1:p.His348Tyr
  • NP_006339.3:p.His617Tyr
  • NP_006339.4:p.His586Tyr
  • NP_859422.3:p.His565Tyr
  • NC_000007.13:g.106888938G>A
  • NG_028095.1:g.321022C>T
  • NM_006348.3:c.1849C>T
Protein change:
H348Y
Links:
dbSNP: rs151129529
NCBI 1000 Genomes Browser:
rs151129529
Molecular consequence:
  • NM_001161520.2:c.1756C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001379511.1:c.1594C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001379512.1:c.1582C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001379513.1:c.1756C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001379514.1:c.1756C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001379515.1:c.1186C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001379516.1:c.1042C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_006348.5:c.1756C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_181733.4:c.1693C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV005394237Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)		Uncertain significance
(Sep 26, 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, SCV005394237.1

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

Description

Variant summary: COG5 c.1756C>T (p.His586Tyr) results in a conservative amino acid change in the encoded protein sequence. Three of three in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 0.00024 in 243846 control chromosomes. This frequency is not significantly higher than estimated for a pathogenic variant in COG5 causing Congenital Disorder Of Glycosylation, Type 2i, allowing no conclusion about variant significance. To our knowledge, no occurrence of c.1756C>T in individuals affected with Congenital Disorder Of Glycosylation, Type 2i and no experimental evidence demonstrating its impact on protein function have been reported. ClinVar contains an entry for this variant (Variation ID: 487322). 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: Nov 18, 2024