NM_018475.5(TMEM165):c.17_18delinsGG (p.Pro6Arg) AND TMEM165-congenital disorder of glycosylation

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jun 22, 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:: RCV002958297.3

Allele description [Variation Report for NM_018475.5(TMEM165):c.17_18delinsGG (p.Pro6Arg)]

NM_018475.5(TMEM165):c.17_18delinsGG (p.Pro6Arg)

Genes:

LOC129992613:ATAC-STARR-seq lymphoblastoid silent region 15439 [Gene]
TMEM165:transmembrane protein 165 [Gene - OMIM - HGNC]

Variant type:

Indel

Cytogenetic location:

4q12

Genomic location:

Preferred name:

NM_018475.5(TMEM165):c.17_18delinsGG (p.Pro6Arg)

HGVS:

NC_000004.12:g.55396206_55396207delinsGG
NG_032881.1:g.5294_5295delinsGG
NG_032881.2:g.5251_5252delinsGG
NM_018475.5:c.17_18delinsGGMANE SELECT
NP_060945.2:p.Pro6Arg
NC_000004.11:g.56262373_56262374delinsGG
NR_073070.2:n.250_251delinsGG

Protein change:

P6R

Molecular consequence:

NM_018475.5:c.17_18delinsGG - missense variant - [Sequence Ontology: SO:0001583]
NR_073070.2:n.250_251delinsGG - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: TMEM165-congenital disorder of glycosylation
Synonyms:: CDG IIk; Congenital disorder of glycosylation type 2k; TMEM165-CDG
Identifiers:: MONDO: MONDO:0013870; MedGen: C3553571; Orphanet: 314667; OMIM: 614727

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003274215	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jun 22, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003274215

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jun 22, 2022)

germline

clinical testing

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

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

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003274215.2

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

Description

Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. This variant has not been reported in the literature in individuals affected with TMEM165-related conditions. Information on the frequency of this variant in the gnomAD database is not available, as this variant may be reported differently in the database. This sequence change replaces proline, which is neutral and non-polar, with arginine, which is basic and polar, at codon 6 of the TMEM165 protein (p.Pro6Arg).

#	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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