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 [Variation Report for NM_001278293.3(ARL6):c.188T>A (p.Leu63Ter)]

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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004593217	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Aug 29, 2023)	germline	clinical testing	PubMed (7) [See all records that cite these PMIDs] 15258860, 19858128, 20142850, 22334370, 27486776, 31736247, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004593217

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Aug 29, 2023)

germline

clinical testing

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

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

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

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical 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.

#	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: Mar 5, 2024

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