NC_000015.9:g.(?_44855319)_(45898712_?)dup AND Arginine:glycine amidinotransferase deficiency

This record was updated by the submitter. Please see the current version.

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Oct 12, 2020
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:: RCV001304383.1

Allele description

NC_000015.9:g.(?_44855319)_(45898712_?)dup

Genes:

PATL2:PAT1 homolog 2 [Gene - OMIM - HGNC]
SPG11:SPG11 vesicle trafficking associated, spatacsin [Gene - OMIM - HGNC]
SHF:Src homology 2 domain containing F [Gene - OMIM - HGNC]
B2M:beta-2-microglobulin [Gene - OMIM - HGNC]
BLOC1S6:biogenesis of lysosomal organelles complex 1 subunit 6 [Gene - OMIM - HGNC]
C15orf48:chromosome 15 open reading frame 48 [Gene - OMIM - HGNC]
DUOX1:dual oxidase 1 [Gene - OMIM - HGNC]
DUOX2:dual oxidase 2 [Gene - OMIM - HGNC]
DUOXA1:dual oxidase maturation factor 1 [Gene - OMIM - HGNC]
DUOXA2:dual oxidase maturation factor 2 [Gene - OMIM - HGNC]
GATM:glycine amidinotransferase [Gene - OMIM - HGNC]
SLC28A2:solute carrier family 28 member 2 [Gene - OMIM - HGNC]
SLC30A4:solute carrier family 30 member 4 [Gene - OMIM - HGNC]
SORD:sorbitol dehydrogenase [Gene - OMIM - HGNC]
SPATA5L1:spermatogenesis associated 5 like 1 [Gene - OMIM - HGNC]
TERB2:telomere repeat binding bouquet formation protein 2 [Gene - OMIM - HGNC]
TRIM69:tripartite motif containing 69 [Gene - OMIM - HGNC]

Variant type:

Duplication

Cytogenetic location:

15q21.1

Genomic location:

Chr15: 44855319 - 45898712 (on Assembly GRCh37)

Preferred name:

NC_000015.9:g.(?_44855319)_(45898712_?)dup

HGVS:

NC_000015.9:g.(?_44855319)_(45898712_?)dup

Condition(s)

Name:: Arginine:glycine amidinotransferase deficiency (CCDS3)
Synonyms:: AGAT deficiency; Creatine deficiency syndrome due to AGAT deficiency; GATM deficiency; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0012996; MedGen: C2675179; Orphanet: 35704; OMIM: 612718

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RecName: Full=Immunoglobulin heavy constant gamma 2; AltName: Full=Ig gamma-2 ch...
RecName: Full=Immunoglobulin heavy constant gamma 2; AltName: Full=Ig gamma-2 chain C region; AltName: Full=Ig gamma-2 chain C region DOT; AltName: Full=Ig gamma-2 chain C region TIL; AltName: Full=Ig gamma-2 chain C region ZIE
gi|2500440430|sp|P01859.3|IGHG2_HUM

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001493660	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Oct 12, 2020)	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

SCV001493660

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Oct 12, 2020)

germline

clinical testing

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

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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 Invitae, SCV001493660.1

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

Description

This variant results in a copy number gain of the genomic region encompassing the full coding sequence of the GATM gene. The boundaries of this event are unknown as they extend beyond the assayed region for this gene and therefore may encompass additional genes. As the precise location of this event is unknown, it may be in tandem or it may be located elsewhere in the genome. This variant has not been reported in the literature in individuals with GATM-related disease. 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: Apr 23, 2022

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