NM_001077418.3(TMEM231):c.164A>G (p.Tyr55Cys) AND multiple conditions

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Apr 29, 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:: RCV002585057.10

Allele description [Variation Report for NM_001077418.3(TMEM231):c.164A>G (p.Tyr55Cys)]

NM_001077418.3(TMEM231):c.164A>G (p.Tyr55Cys)

Genes:

LOC130059440:ATAC-STARR-seq lymphoblastoid silent region 7724 [Gene]
TMEM231:transmembrane protein 231 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

16q23.1

Genomic location:

Preferred name:

NM_001077418.3(TMEM231):c.164A>G (p.Tyr55Cys)

HGVS:

NC_000016.10:g.75555949T>C
NG_033109.1:g.5338A>G
NG_193861.1:g.107T>C
NM_001077416.2:c.323A>G
NM_001077418.3:c.164A>GMANE SELECT
NP_001070884.2:p.Tyr108Cys
NP_001070886.1:p.Tyr55Cys
NC_000016.9:g.75589847T>C
NR_074083.2:n.207A>G

Protein change:

Y108C

Molecular consequence:

NM_001077416.2:c.323A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001077418.3:c.164A>G - missense variant - [Sequence Ontology: SO:0001583]
NR_074083.2:n.207A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Joubert syndrome 20 (JBTS20)
Identifiers:: MONDO: MONDO:0013994; MedGen: C3554235; Orphanet: 475; OMIM: 614970

Name:: Meckel syndrome, type 11 (MKS11)
Identifiers:: MONDO: MONDO:0014164; MedGen: C3809352; Orphanet: 564; OMIM: 615397

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003489297	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Apr 29, 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

SCV003489297

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Apr 29, 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, SCV003489297.2

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

Description

This sequence change replaces tyrosine, which is neutral and polar, with cysteine, which is neutral and slightly polar, at codon 108 of the TMEM231 protein (p.Tyr108Cys). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This variant has not been reported in the literature in individuals affected with TMEM231-related conditions. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Not Available"; Align-GVGD: "Class C55"). 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.

#	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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