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NM_001278293.3(ARL6):c.188T>A (p.Leu63Ter) AND multiple conditions

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Aug 29, 2023
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:
RCV003800281.1

Allele description

NM_001278293.3(ARL6):c.188T>A (p.Leu63Ter)

Gene:
ARL6:ADP ribosylation factor like GTPase 6 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
3q11.2
Genomic location:
Preferred name:
NM_001278293.3(ARL6):c.188T>A (p.Leu63Ter)
HGVS:
  • NC_000003.12:g.97780617T>A
  • NG_008119.2:g.20867T>A
  • NM_001278293.3:c.188T>AMANE SELECT
  • NM_001323513.2:c.188T>A
  • NM_001323514.2:c.188T>A
  • NM_032146.5:c.188T>A
  • NM_177976.3:c.188T>A
  • NP_001265222.1:p.Leu63Ter
  • NP_001310442.1:p.Leu63Ter
  • NP_001310443.1:p.Leu63Ter
  • NP_115522.1:p.Leu63Ter
  • NP_816931.1:p.Leu63Ter
  • NC_000003.11:g.97499461T>A
  • NR_103511.3:n.534T>A
  • NR_136595.2:n.534T>A
  • NR_136597.2:n.435T>A
  • NR_136598.2:n.435T>A
  • NR_136600.3:n.435T>A
  • NR_136601.3:n.435T>A
  • NR_136602.3:n.435T>A
Protein change:
L63*
Molecular consequence:
  • NR_103511.3:n.534T>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_136595.2:n.534T>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_136597.2:n.435T>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_136598.2:n.435T>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_136600.3:n.435T>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_136601.3:n.435T>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_136602.3:n.435T>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NM_001278293.3:c.188T>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001323513.2:c.188T>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001323514.2:c.188T>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_032146.5:c.188T>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_177976.3:c.188T>A - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:
Bardet-Biedl syndrome 3 (BBS3)
Identifiers:
MONDO: MONDO:0010832; MedGen: C1859564; Orphanet: 110; OMIM: 600151
Name:
Retinitis pigmentosa 55 (RP55)
Identifiers:
MONDO: MONDO:0013312; MedGen: C3150808; Orphanet: 791; OMIM: 613575

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004593217Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Aug 29, 2023) 		germlineclinical testing

PubMed (7)
[See all records that cite these PMIDs]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Comparative genomic analysis identifies an ADP-ribosylation factor-like gene as the cause of Bardet-Biedl syndrome (BBS3).

Chiang AP, Nishimura D, Searby C, Elbedour K, Carmi R, Ferguson AL, Secrist J, Braun T, Casavant T, Stone EM, Sheffield VC.

Am J Hum Genet. 2004 Sep;75(3):475-84. Epub 2004 Jul 16.

PubMed [citation]
PMID:
15258860
PMCID:
PMC1182025

Clinical and molecular characterisation of Bardet-Biedl syndrome in consanguineous populations: the power of homozygosity mapping.

Abu Safieh L, Aldahmesh MA, Shamseldin H, Hashem M, Shaheen R, Alkuraya H, Al Hazzaa SA, Al-Rajhi A, Alkuraya FS.

J Med Genet. 2010 Apr;47(4):236-41. doi: 10.1136/jmg.2009.070755. Epub 2009 Oct 26.

PubMed [citation]
PMID:
19858128
See all PubMed Citations (7)

Details of each submission

From Invitae, SCV004593217.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (7)

Description

This sequence change creates a premature translational stop signal (p.Leu63*) in the ARL6 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in ARL6 are known to be pathogenic (PMID: 15258860, 19858128, 20142850, 22334370, 27486776, 31736247). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with ARL6-related conditions. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. For these reasons, this variant has been classified as Pathogenic.

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

Last Updated: Mar 5, 2024