NM_001044385.3(TMEM237):c.26T>A (p.Leu9Gln) AND Joubert syndrome 14

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 15, 2021
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:: RCV001964905.6

Allele description [Variation Report for NM_001044385.3(TMEM237):c.26T>A (p.Leu9Gln)]

NM_001044385.3(TMEM237):c.26T>A (p.Leu9Gln)

Genes:

LOC129935417:ATAC-STARR-seq lymphoblastoid silent region 12235 [Gene]
TMEM237:transmembrane protein 237 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

2q33.1

Genomic location:

Preferred name:

NM_001044385.3(TMEM237):c.26T>A (p.Leu9Gln)

HGVS:

NC_000002.12:g.201643375A>T
NG_012654.1:g.60320T>A
NG_032049.1:g.5155T>A
NM_001044385.3:c.26T>AMANE SELECT
NP_001037850.1:p.Leu9Gln
NC_000002.11:g.202508098A>T

Protein change:

L9Q

Links:

dbSNP: rs2105906100

NCBI 1000 Genomes Browser:

rs2105906100

Molecular consequence:

NM_001044385.3:c.26T>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Joubert syndrome 14 (JBTS14)
Identifiers:: MONDO: MONDO:0013745; MedGen: C3280766; OMIM: 614424

Recent activity

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D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform X16 [Homo sapiens]
D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform X16 [Homo sapiens]
gi|2462576692|ref|XP_054199672.1|

Protein
zinc finger and BTB domain-containing protein 24 isoform X1 [Rattus norvegicus]
zinc finger and BTB domain-containing protein 24 isoform X1 [Rattus norvegicus]
gi|1958757699|ref|XP_038954835.1|

Protein
Large-scale analysis of novel cellular microbes from the plant biome
Large-scale analysis of novel cellular microbes from the plant biome
Large-scale analysis of novel cellular microbes from the plant biome

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002204168	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Aug 15, 2021)	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

SCV002204168

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Aug 15, 2021)

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, SCV002204168.3

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

Description

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. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. 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: "Benign"; Align-GVGD: "Class C0"). This variant has not been reported in the literature in individuals affected with TMEM237-related conditions. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate insufficient coverage at this position in the ExAC database. This sequence change replaces leucine with glutamine at codon 9 of the TMEM237 protein (p.Leu9Gln). The leucine residue is weakly conserved and there is a moderate physicochemical difference between leucine and glutamine.

#	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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