NM_001174150.2(ARL13B):c.200T>G (p.Val67Gly) AND Joubert syndrome 8

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: May 19, 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:: RCV003022683.3

Allele description [Variation Report for NM_001174150.2(ARL13B):c.200T>G (p.Val67Gly)]

NM_001174150.2(ARL13B):c.200T>G (p.Val67Gly)

Gene:

ARL13B:ARF like GTPase 13B [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

3q11.2

Genomic location:

Preferred name:

NM_001174150.2(ARL13B):c.200T>G (p.Val67Gly)

HGVS:

NC_000003.12:g.94003728T>G
NG_017076.1:g.28590T>G
NM_001174150.2:c.200T>GMANE SELECT
NM_001174151.2:c.-110T>G
NM_001321328.2:c.155T>G
NM_001410782.1:c.200T>G
NM_144996.4:c.59+23246T>G
NM_182896.3:c.200T>G
NP_001167621.1:p.Val67Gly
NP_001308257.1:p.Val52Gly
NP_001397711.1:p.Val67Gly
NP_878899.1:p.Val67Gly
NC_000003.11:g.93722572T>G

Protein change:

V52G

Molecular consequence:

NM_001174151.2:c.-110T>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_144996.4:c.59+23246T>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001174150.2:c.200T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001321328.2:c.155T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001410782.1:c.200T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_182896.3:c.200T>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Joubert syndrome 8 (JBTS8)
Identifiers:: MONDO: MONDO:0012855; MedGen: C2676771; Orphanet: 475; OMIM: 612291

Recent activity

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vomeronasal receptor Vmn2r22 precursor [Mus musculus]
vomeronasal receptor Vmn2r22 precursor [Mus musculus]
gi|157277998|ref|NP_001098107.1|

Protein
Mthfs 5, 10-methenyltetrahydrofolate synthetase [Mus musculus]
Mthfs 5, 10-methenyltetrahydrofolate synthetase [Mus musculus]
Gene ID:107885

Gene
C630050I24Rik RIKEN cDNA C630050I24 gene [Mus musculus]
C630050I24Rik RIKEN cDNA C630050I24 gene [Mus musculus]
Gene ID:78571

Gene
Angptl6 angiopoietin-like 6 [Mus musculus]
Angptl6 angiopoietin-like 6 [Mus musculus]
Gene ID:70726

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003323945	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (May 19, 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

SCV003323945

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(May 19, 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, SCV003323945.2

#	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 valine, which is neutral and non-polar, with glycine, which is neutral and non-polar, at codon 67 of the ARL13B protein (p.Val67Gly). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with ARL13B-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: "Probably Damaging"; Align-GVGD: "Class C0"). 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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