NM_015386.3(COG4):c.373C>T (p.Arg125Cys) AND Inborn genetic diseases

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Dec 28, 2020
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:: RCV002551587.2

Allele description [Variation Report for NM_015386.3(COG4):c.373C>T (p.Arg125Cys)]

NM_015386.3(COG4):c.373C>T (p.Arg125Cys)

Gene:

COG4:component of oligomeric golgi complex 4 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

16q22.1

Genomic location:

Preferred name:

NM_015386.3(COG4):c.373C>T (p.Arg125Cys)

HGVS:

NC_000016.10:g.70514506G>A
NG_027529.1:g.14049C>T
NM_001195139.2:c.361C>T
NM_001365426.1:c.-54C>T
NM_015386.3:c.373C>TMANE SELECT
NP_001182068.2:p.Arg121Cys
NP_056201.2:p.Arg125Cys
NC_000016.9:g.70548409G>A
NM_015386.2:c.373C>T
NR_158212.1:n.384C>T

Protein change:

R121C

Links:

dbSNP: rs757774654

NCBI 1000 Genomes Browser:

rs757774654

Molecular consequence:

NM_001365426.1:c.-54C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001195139.2:c.361C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_015386.3:c.373C>T - missense variant - [Sequence Ontology: SO:0001583]
NR_158212.1:n.384C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

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
SCV003677743	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Uncertain significance (Dec 28, 2020)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003677743

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Uncertain significance
(Dec 28, 2020)

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, SCV003677743.2

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

Description

The c.373C>T (p.R125C) alteration is located in exon 4 (coding exon 4) of the COG4 gene. This alteration results from a C to T substitution at nucleotide position 373, causing the arginine (R) at amino acid position 125 to be replaced by a cysteine (C). The in silico prediction for the p.R125C alteration is inconclusive. 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: May 1, 2024

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