NM_000045.4(ARG1):c.314_345delinsATGCAAGCATCAGGATGACT (p.Ile105_His115delinsAsnAlaSerIleArgMetThr) AND not provided

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Feb 10, 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:: RCV003317591.8

Allele description [Variation Report for NM_000045.4(ARG1):c.314_345delinsATGCAAGCATCAGGATGACT (p.Ile105_His115delinsAsnAlaSerIleArgMetThr)]

NM_000045.4(ARG1):c.314_345delinsATGCAAGCATCAGGATGACT (p.Ile105_His115delinsAsnAlaSerIleArgMetThr)

Genes:

ARG1:arginase 1 [Gene - OMIM - HGNC]
MED23:mediator complex subunit 23 [Gene - OMIM - HGNC]

Variant type:

Indel

Cytogenetic location:

6q23.2

Genomic location:

Preferred name:

NM_000045.4(ARG1):c.314_345delinsATGCAAGCATCAGGATGACT (p.Ile105_His115delinsAsnAlaSerIleArgMetThr)

HGVS:

NC_000006.12:g.131581227_131581258delinsATGCAAGCATCAGGATGACT
NG_007086.2:g.13003_13034delinsATGCAAGCATCAGGATGACT
NG_031860.2:g.51966_51997delinsAGTCATCCTGATGCTTGCAT
NM_000045.4:c.314_345delinsATGCAAGCATCAGGATGACTMANE SELECT
NM_001244438.2:c.338_369delinsATGCAAGCATCAGGATGACT
NM_001270521.2:c.4077+6451_4077+6482delinsAGTCATCCTGATGCTTGCAT
NM_001369020.1:c.306-1833_306-1802delinsATGCAAGCATCAGGATGACT
NM_015979.4:c.4095+6451_4095+6482delinsAGTCATCCTGATGCTTGCAT
NP_000036.2:p.Ile105_His115delinsAsnAlaSerIleArgMetThr
NP_001231367.1:p.Ile113_His123delinsAsnAlaSerIleArgMetThr
NC_000006.11:g.131902367_131902398delinsATGCAAGCATCAGGATGACT
NM_000045.2:c.314_345delinsATGCAAGCATCAGGATGACT
NM_000045.3:c.314_345delinsATGCAAGCATCAGGATGACT
NR_160934.1:n.298_329delinsATGCAAGCATCAGGATGACT

Molecular consequence:

NM_000045.4:c.314_345delinsATGCAAGCATCAGGATGACT - inframe_indel - [Sequence Ontology: SO:0001820]
NM_001244438.2:c.338_369delinsATGCAAGCATCAGGATGACT - inframe_indel - [Sequence Ontology: SO:0001820]
NM_001270521.2:c.4077+6451_4077+6482delinsAGTCATCCTGATGCTTGCAT - intron variant - [Sequence Ontology: SO:0001627]
NM_001369020.1:c.306-1833_306-1802delinsATGCAAGCATCAGGATGACT - intron variant - [Sequence Ontology: SO:0001627]
NM_015979.4:c.4095+6451_4095+6482delinsAGTCATCCTGATGCTTGCAT - intron variant - [Sequence Ontology: SO:0001627]
NR_160934.1:n.298_329delinsATGCAAGCATCAGGATGACT - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004021612	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Likely pathogenic (Feb 10, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004021612

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Likely pathogenic
(Feb 10, 2023)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From GeneDx, SCV004021612.1

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

Description

In-frame deletion of 11 amino acids and insertion of 7 amino acids in a non-repeat region; Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge

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

Last Updated: May 26, 2024

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Relating variation to medicine