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NM_015979.4(MED23):c.4095+4355_4095+4358del AND Arginase deficiency

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jul 26, 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:
RCV002891181.9

Allele description [Variation Report for NM_015979.4(MED23):c.4095+4355_4095+4358del]

NM_015979.4(MED23):c.4095+4355_4095+4358del

Genes:
ARG1:arginase 1 [Gene - OMIM - HGNC]
MED23:mediator complex subunit 23 [Gene - OMIM - HGNC]
Variant type:
Microsatellite
Cytogenetic location:
6q23.2
Genomic location:
Preferred name:
NM_015979.4(MED23):c.4095+4355_4095+4358del
HGVS:
  • NC_000006.12:g.131583354GAAA[1]
  • NG_007086.2:g.15130GAAA[1]
  • NG_031860.2:g.49866CTTT[1]
  • NM_001270521.2:c.4077+4355_4077+4358del
  • NM_015979.4:c.4095+4355_4095+4358del
  • NC_000006.11:g.131904491_131904494del
  • NC_000006.11:g.131904494GAAA[1]
Molecular consequence:
  • NM_001270521.2:c.4077+4355_4077+4358del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_015979.4:c.4095+4355_4095+4358del - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:
Arginase deficiency
Synonyms:
ARG1 deficiency; Argininemia
Identifiers:
MONDO: MONDO:0008814; MedGen: C0268548; Orphanet: 90; OMIM: 207800

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003247813Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Jul 26, 2022) 		germlineclinical testing

PubMed (3)
[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

Molecular basis of phenotypic variation in patients with argininemia.

Uchino T, Snyderman SE, Lambert M, Qureshi IA, Shapira SK, Sansaricq C, Smit LM, Jakobs C, Matsuda I.

Hum Genet. 1995 Sep;96(3):255-60.

PubMed [citation]
PMID:
7649538

Mouse model for human arginase deficiency.

Iyer RK, Yoo PK, Kern RM, Rozengurt N, Tsoa R, O'Brien WE, Yu H, Grody WW, Cederbaum SD.

Mol Cell Biol. 2002 Jul;22(13):4491-8.

PubMed [citation]
PMID:
12052859
PMCID:
PMC133904
See all PubMed Citations (3)

Details of each submission

From Invitae, SCV003247813.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

This sequence change creates a premature translational stop signal (p.Lys224Glyfs*5) in the ARG1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in ARG1 are known to be pathogenic (PMID: 7649538, 12052859). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with ARG1-related conditions. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus 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: Apr 20, 2024