NC_000016.9:g.(?_56226148)_(57286179_?)del AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Oct 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:: RCV004582872.2

Allele description [Variation Report for NC_000016.9:g.(?_56226148)_(57286179_?)del]

NC_000016.9:g.(?_56226148)_(57286179_?)del

Genes:

OGFOD1:2-oxoglutarate and iron dependent oxygenase domain containing 1 [Gene - OMIM - HGNC]
ARL2BP:ARF like GTPase 2 binding protein [Gene - OMIM - HGNC]
BBS2:Bardet-Biedl syndrome 2 [Gene - OMIM - HGNC]
GNAO1:G protein subunit alpha o1 [Gene - OMIM - HGNC]
NLRC5:NLR family CARD domain containing 5 [Gene - OMIM - HGNC]
AMFR:autocrine motility factor receptor [Gene - OMIM - HGNC]
CETP:cholesteryl ester transfer protein [Gene - OMIM - HGNC]
CPNE2:copine 2 [Gene - OMIM - HGNC]
HERPUD1:homocysteine inducible ER protein with ubiquitin like domain 1 [Gene - OMIM - HGNC]
MT1A:metallothionein 1A [Gene - OMIM - HGNC]
MT1B:metallothionein 1B [Gene - OMIM - HGNC]
MT1E:metallothionein 1E [Gene - OMIM - HGNC]
MT1F:metallothionein 1F [Gene - OMIM - HGNC]
MT1G:metallothionein 1G [Gene - OMIM - HGNC]
MT1H:metallothionein 1H [Gene - OMIM - HGNC]
MT1M:metallothionein 1M [Gene - OMIM - HGNC]
MT1X:metallothionein 1X [Gene - OMIM - HGNC]
MT2A:metallothionein 2A [Gene - OMIM - HGNC]
MT3:metallothionein 3 [Gene - OMIM - HGNC]
MT4:metallothionein 4 [Gene - OMIM - HGNC]
MIR138-2:microRNA 138-2 [Gene - OMIM - HGNC]
NUP93:nucleoporin 93 [Gene - OMIM - HGNC]
NUDT21:nudix hydrolase 21 [Gene - OMIM - HGNC]
PSME3IP1:proteasome activator subunit 3 interacting protein 1 [Gene - OMIM - HGNC]
RSPRY1:ring finger and SPRY domain containing 1 [Gene - OMIM - HGNC]
SLC12A3:solute carrier family 12 member 3 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

16q12.2-13

Genomic location:

Chr16: 56226148 - 57286179 (on Assembly GRCh37)

Preferred name:

NC_000016.9:g.(?_56226148)_(57286179_?)del

HGVS:

NC_000016.9:g.(?_56226148)_(57286179_?)del

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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MULTISPECIES: membrane protein insertion efficiency factor YidD [Diaphorobacter]
MULTISPECIES: membrane protein insertion efficiency factor YidD [Diaphorobacter]
gi|1518836142|ref|WP_123675436.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV005063953	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Oct 19, 2022)	unknown	clinical testing	PubMed (5) [See all records that cite these PMIDs] 23849777, 27790702, 29718757, 30210231, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV005063953

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Oct 19, 2022)

unknown

clinical testing

PubMed (5)
[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	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Mutations in ARL2BP, encoding ADP-ribosylation-factor-like 2 binding protein, cause autosomal-recessive retinitis pigmentosa.

Davidson AE, Schwarz N, Zelinger L, Stern-Schneider G, Shoemark A, Spitzbarth B, Gross M, Laxer U, Sosna J, Sergouniotis PI, Waseem NH, Wilson R, Kahn RA, Plagnol V, Wolfrum U, Banin E, Hardcastle AJ, Cheetham ME, Sharon D, Webster AR.

Am J Hum Genet. 2013 Aug 8;93(2):321-9. doi: 10.1016/j.ajhg.2013.06.003. Epub 2013 Jul 11.

PubMed [citation]

PMID:: 23849777
PMCID:: PMC3738823

ARL2BP mutations account for 0.1% of autosomal recessive rod-cone dystrophies with the report of a novel splice variant.

Audo I, El Shamieh S, Méjécase C, Michiels C, Demontant V, Antonio A, Condroyer C, Boyard F, Letexier M, Saraiva JP, Blanchard S, Mohand-Saïd S, Sahel JA, Zeitz C.

Clin Genet. 2017 Jul;92(1):109-111. doi: 10.1111/cge.12909. Epub 2017 Feb 6.

PubMed [citation]

PMID:: 27790702

See all PubMed Citations (5)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV005063953.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (5)

Description

For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals affected with ARL2BP-related conditions. A gross deletion of the genomic region encompassing the full coding sequence of the ARL2BP gene has been identified. Loss-of-function variants in ARL2BP are known to be pathogenic (PMID: 23849777, 27790702, 29718757, 30210231). The boundaries of this event are unknown as they extend beyond the assayed region for this gene and therefore may encompass additional genes.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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