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NM_001174150.2(ARL13B):c.1250A>C (p.Gln417Pro) AND Joubert syndrome 8

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Oct 24, 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:
RCV002638506.1

Allele description

NM_001174150.2(ARL13B):c.1250A>C (p.Gln417Pro)

Gene:
ARL13B:ADP ribosylation factor like GTPase 13B [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
3q11.2
Genomic location:
Preferred name:
NM_001174150.2(ARL13B):c.1250A>C (p.Gln417Pro)
HGVS:
  • NC_000003.12:g.94053226A>C
  • NG_017076.1:g.78088A>C
  • NM_001174150.2:c.1250A>CMANE SELECT
  • NM_001174151.2:c.941A>C
  • NM_001321328.2:c.1205A>C
  • NM_001410782.1:c.1181A>C
  • NM_144996.4:c.929A>C
  • NM_182896.3:c.1250A>C
  • NP_001167621.1:p.Gln417Pro
  • NP_001167622.1:p.Gln314Pro
  • NP_001308257.1:p.Gln402Pro
  • NP_001397711.1:p.Gln394Pro
  • NP_659433.2:p.Gln310Pro
  • NP_878899.1:p.Gln417Pro
  • NC_000003.11:g.93772070A>C
  • NR_033427.2:n.1274A>C
  • NR_135621.2:n.1265A>C
Protein change:
Q310P
Molecular consequence:
  • NM_001174150.2:c.1250A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001174151.2:c.941A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001321328.2:c.1205A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001410782.1:c.1181A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_144996.4:c.929A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_182896.3:c.1250A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NR_033427.2:n.1274A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_135621.2:n.1265A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

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

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003521179Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Oct 24, 2022) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical 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 Invitae, SCV003521179.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

This sequence change replaces glutamine, which is neutral and polar, with proline, which is neutral and non-polar, at codon 417 of the ARL13B protein (p.Gln417Pro). This variant is present in population databases (rs754535814, gnomAD 0.04%). 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: "Benign"; 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.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Feb 13, 2023