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NM_000022.4(ADA):c.956_960del (p.Glu319fs)

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Interpretation:
Pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
11 (Most recent: Nov 19, 2021)
Last evaluated:
Aug 10, 2021
Accession:
VCV000193544.14
Variation ID:
193544
Description:
5bp deletion
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NM_000022.4(ADA):c.956_960del (p.Glu319fs)

Allele ID
190708
Variant type
Deletion
Variant length
5 bp
Cytogenetic location
20q13.12
Genomic location
20: 44621033-44621037 (GRCh38) GRCh38 UCSC
20: 43249674-43249678 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_16:g.35699_35703del
LRG_16t1:c.956_960del
NM_000022.4:c.956_960delAAGAG MANE Select
... more HGVS
Protein change
E184fs, E295fs, E319fs
Other names
-
Canonical SPDI
NC_000020.11:44621032:CTCTTC:C
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
ClinGen: CA274927
dbSNP: rs771266745
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic 3 criteria provided, multiple submitters, no conflicts Jan 1, 2021 RCV000255208.6
Pathogenic 8 criteria provided, multiple submitters, no conflicts Aug 10, 2021 RCV000173618.11
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
ADA - - GRCh38
GRCh37
281 344

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Pathogenic
(Oct 08, 2020)
criteria provided, single submitter
Method: clinical testing
Severe combined immunodeficiency due to ADA deficiency
Allele origin: germline
Invitae
Accession: SCV001200277.2
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (4)
Comment:
This sequence change creates a premature translational stop signal (p.Glu319Glyfs*3) in the ADA gene. It is expected to result in an absent or disrupted protein … (more)
Pathogenic
(Sep 24, 2014)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000224743.5
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Pathogenic
(Feb 20, 2020)
criteria provided, single submitter
Method: clinical testing
Severe combined immunodeficiency due to ADA deficiency
Allele origin: germline
Johns Hopkins Genomics, Johns Hopkins University
Accession: SCV001425436.1
Submitted: (May 28, 2020)
Evidence details
Publications
PubMed (3)
Pathogenic
(Jan 01, 2021)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
CeGaT Praxis fuer Humangenetik Tuebingen
Accession: SCV001500263.3
Submitted: (Jul 04, 2021)
Evidence details
Pathogenic
(Feb 06, 2019)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000321381.6
Submitted: (Sep 25, 2021)
Evidence details
Comment:
Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; This … (more)
Pathogenic
(Aug 10, 2021)
criteria provided, single submitter
Method: clinical testing
Severe combined immunodeficiency due to ADA deficiency
Allele origin: germline
Nilou-Genome Lab
Accession: SCV001977471.1
Submitted: (Oct 12, 2021)
Evidence details
Pathogenic
(Dec 30, 2016)
criteria provided, single submitter
Method: clinical testing
Severe combined immunodeficiency due to ADA deficiency
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV000693974.1
Submitted: (Jan 25, 2018)
Evidence details
Publications
PubMed (3)
Comment:
Variant summary: The ADA c.956_960delAAGAG (p.Glu319Glyfs) variant results in a premature termination codon, predicted to cause a truncated or absent ADA protein due to nonsense … (more)
Pathogenic
(Nov 16, 2020)
no assertion criteria provided
Method: curation
Severe combined immunodeficiency due to ADA deficiency
(Autosomal recessive inheritance)
Allele origin: germline
Broad Institute Rare Disease Group, Broad Institute
Accession: SCV001445938.1
Submitted: (Nov 17, 2020)
Evidence details
Publications
PubMed (3)
Comment:
This heterozygous p.Glu319GlyfsTer3 variant in ADA was identified by our study in an individual with severe combined immunodeficiency due to adenosine deaminase deficiency in the … (more)
Pathogenic
(Sep 16, 2020)
no assertion criteria provided
Method: clinical testing
Severe combined immunodeficiency due to ADA deficiency
Allele origin: germline
Natera, Inc.
Accession: SCV001460804.1
Submitted: (Dec 28, 2020)
Evidence details
Pathogenic
(Oct 29, 2021)
no assertion criteria provided
Method: clinical testing
Severe combined immunodeficiency due to ADA deficiency
Allele origin: germline
PerkinElmer Genomics
Accession: SCV002021871.1
Submitted: (Nov 19, 2021)
Evidence details
Likely pathogenic
(Oct 31, 2016)
no assertion criteria provided
Method: clinical testing
Severe combined immunodeficiency due to ADA deficiency
Allele origin: unknown
Counsyl
Accession: SCV000485744.2
Submitted: (Aug 05, 2019)
Evidence details
Publications
PubMed (1)

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
Rapid molecular diagnostics of severe primary immunodeficiency determined by using targeted next-generation sequencing. Yu H The Journal of allergy and clinical immunology 2016 PMID: 27484032
Update on the safety and efficacy of retroviral gene therapy for immunodeficiency due to adenosine deaminase deficiency. Cicalese MP Blood 2016 PMID: 27129325
Diagnosis, Treatment and Long-Term Follow Up of Patients with ADA Deficiency: a Single-Center Experience. Baffelli R Journal of clinical immunology 2015 PMID: 26376800
Spectrum of mutations in a cohort of UK patients with ADA deficient SCID: Segregation of genotypes with specific ethnicities. Adams SP Clinical immunology (Orlando, Fla.) 2015 PMID: 26255240
Severe phenotype of severe combined immunodeficiency caused by adenosine deaminase deficiency in a patient with a homozygous mutation due to uniparental disomy. Geelen J The Journal of allergy and clinical immunology 2013 PMID: 23260757
Two new mutations at the adenosine deaminase (ADA) locus (Q254X and del nt1050-54) unusual for not being missense mutations. Hirschhorn R Human mutation 1993 PMID: 8401541
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=ADA - - - -

Text-mined citations for rs771266745...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Nov 28, 2021