ClinVar Genomic variation as it relates to human health
NM_000022.4(ADA):c.478+1G>A
The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.
Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_000022.4(ADA):c.478+1G>A
Variation ID: 265025 Accession: VCV000265025.31
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 20q13.12 20: 44625568 (GRCh38) [ NCBI UCSC ] 20: 43254209 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
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First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.
Last submission Help The date of the most recent submission for each type of classification for this variant.
Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline Apr 4, 2013 Jul 23, 2024 Feb 11, 2024 - HGVS
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Nucleotide Protein Molecular
consequenceNM_000022.4:c.478+1G>A MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
splice donor NM_001322050.2:c.73+888G>A intron variant NM_001322051.2:c.478+1G>A splice donor NC_000020.11:g.44625568C>T NC_000020.10:g.43254209C>T NG_007385.1:g.31168G>A LRG_16:g.31168G>A LRG_16t1:c.478+1G>A - Protein change
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- Other names
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IVS5DS, G-A, +1
- Canonical SPDI
- NC_000020.11:44625567:C:T
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Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
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Global minor allele
frequency (GMAF) HelpThe global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.
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Allele frequency
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The frequency of the allele represented by this VCV record.
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The Genome Aggregation Database (gnomAD), exomes 0.00002
The Genome Aggregation Database (gnomAD) 0.00003
Trans-Omics for Precision Medicine (TOPMed) 0.00003
Exome Aggregation Consortium (ExAC) 0.00007
- Links
Genes
Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
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Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
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HI score
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The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
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The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
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The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
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The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene. |
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ADA | - | - |
GRCh38 GRCh37 |
531 | 685 |
Conditions - Germline
Condition
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The condition for this variant-condition (RCV) record in ClinVar. |
Classification
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The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions) |
Review status
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The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. |
Last evaluated
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The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
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The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
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Pathogenic (7) |
criteria provided, multiple submitters, no conflicts
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Feb 11, 2024 | RCV000002055.28 | |
Pathogenic (1) |
criteria provided, single submitter
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Mar 28, 2017 | RCV000254941.9 | |
Pathogenic (1) |
criteria provided, single submitter
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Mar 23, 2020 | RCV001731467.9 |
Submissions - Germline
Classification
Help
The submitted germline classification for each SCV record. (Last evaluated) |
Review status
Help
Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria) |
Condition
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The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant. |
Submitter
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The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar. |
More information
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This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter. |
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Pathogenic
(Mar 28, 2017)
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criteria provided, single submitter
Method: clinical testing
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Not Provided
Affected status: yes
Allele origin:
germline
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GeneDx
Accession: SCV000321375.6
First in ClinVar: Oct 10, 2016 Last updated: Oct 10, 2016 |
Comment:
The c.478+1 G>A splice site variant in the ADA gene has been previously reported in association with adenosine deaminase deficiency (Santisteban et al., 1995; Grunebaum … (more)
The c.478+1 G>A splice site variant in the ADA gene has been previously reported in association with adenosine deaminase deficiency (Santisteban et al., 1995; Grunebaum et al., 2012). This pathogenic variant destroys the canonical splice donor site in intron 5, and has been shown to cause abnormal gene splicing (Santisteban et al., 1995). The variant was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. (less)
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Pathogenic
(Mar 23, 2020)
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criteria provided, single submitter
Method: clinical testing
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Severe Combined Immune Deficiency
Affected status: unknown
Allele origin:
germline
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Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV001339001.1
First in ClinVar: Jun 22, 2020 Last updated: Jun 22, 2020 |
Comment:
Variant summary: ADA c.478+1G>A is located in a canonical splice-site and is predicted to affect mRNA splicing resulting in a significantly altered protein due to … (more)
Variant summary: ADA c.478+1G>A is located in a canonical splice-site and is predicted to affect mRNA splicing resulting in a significantly altered protein due to either exon skipping, shortening, or inclusion of intronic material. Several computational tools predict a significant impact on normal splicing: Four predict the variant abolishes a 5 splicing donor site. At least two publications report experimental evidence that this variant affects mRNA splicing and results in deletion of exon 5 (Santisteban_1995, Hirschhorn_1996). The variant allele was found at a frequency of 2.1e-05 in 193792 control chromosomes (gnomAD). c.478+1G>A has been reported in the literature in individuals affected with Severe Combined Immunodeficiency Syndrome (Santisteban_1995, Hirschhorn_1996, Gaspar_2011). These data indicate that the variant may be associated with disease. Two ClinVar submitters (evaluation after 2014) cite the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. (less)
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Pathogenic
(Aug 10, 2021)
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criteria provided, single submitter
Method: clinical testing
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Severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-negative, NK cell-negative, due to adenosine deaminase deficiency
Affected status: no
Allele origin:
germline
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Genome-Nilou Lab
Accession: SCV001977509.1
First in ClinVar: Oct 16, 2021 Last updated: Oct 16, 2021 |
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Pathogenic
(Oct 27, 2021)
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criteria provided, single submitter
Method: clinical testing
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Severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-negative, NK cell-negative, due to adenosine deaminase deficiency
Affected status: unknown
Allele origin:
unknown
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Myriad Genetics, Inc.
Accession: SCV002060164.2
First in ClinVar: Jan 15, 2022 Last updated: Nov 29, 2022 |
Comment:
NM_000022.2(ADA):c.478+1G>A is a canonical splice variant classified as pathogenic in the context of adenosine deaminase deficiency. c.478+1G>A has been observed in cases with relevant disease … (more)
NM_000022.2(ADA):c.478+1G>A is a canonical splice variant classified as pathogenic in the context of adenosine deaminase deficiency. c.478+1G>A has been observed in cases with relevant disease (PMID: 7599635, 22968453). Functional assessments of this variant are available in the literature (PMID: 7599635). c.478+1G>A has been observed in population frequency databases (gnomAD: NFE 0.01%). In summary, NM_000022.2(ADA):c.478+1G>A is a canonical splice variant in a gene where loss of function is a known mechanism of disease, is predicted to disrupt protein function, and has been observed more frequently in cases with the relevant disease than in healthy populations. Please note: this variant was assessed in the context of healthy population screening. (less)
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Pathogenic
(Nov 20, 2023)
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criteria provided, single submitter
Method: clinical testing
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Severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-negative, NK cell-negative, due to adenosine deaminase deficiency
Affected status: unknown
Allele origin:
germline
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Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV001384429.5
First in ClinVar: Jul 16, 2020 Last updated: Feb 14, 2024 |
Comment:
This sequence change affects a donor splice site in intron 5 of the ADA gene. It is expected to disrupt RNA splicing. Variants that disrupt … (more)
This sequence change affects a donor splice site in intron 5 of the ADA gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in ADA are known to be pathogenic (PMID: 26255240, 26376800). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. Disruption of this splice site has been observed in individual(s) with adenosine deaminase deficiency (PMID: 7599635, 8673127). This variant is also known as c.573+1G>A and IVS5+1GT>AT. ClinVar contains an entry for this variant (Variation ID: 265025). 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. (less)
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Pathogenic
(Feb 11, 2024)
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criteria provided, single submitter
Method: clinical testing
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Severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-negative, NK cell-negative, due to adenosine deaminase deficiency
Affected status: unknown
Allele origin:
unknown
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Baylor Genetics
Accession: SCV004213334.2
First in ClinVar: Dec 30, 2023 Last updated: Jun 17, 2024 |
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Pathogenic
(May 26, 2020)
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criteria provided, single submitter
Method: clinical testing
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Severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-negative, NK cell-negative, due to adenosine deaminase deficiency
(Autosomal recessive inheritance)
Affected status: unknown
Allele origin:
germline
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Victorian Clinical Genetics Services, Murdoch Childrens Research Institute
Additional submitter:
Shariant Australia, Australian Genomics
Accession: SCV002557227.2
First in ClinVar: Aug 08, 2022 Last updated: Jul 23, 2024 |
Comment:
Based on the classification scheme VCGS_Germline_v1.1.1, this variant is classified as Pathogenic. Following criteria are met: 0102 - Loss-of-function is a known mechanism of disease … (more)
Based on the classification scheme VCGS_Germline_v1.1.1, this variant is classified as Pathogenic. Following criteria are met: 0102 - Loss-of-function is a known mechanism of disease for this gene. (N) 0106 - This gene is known to be associated with autosomal recessive disease. (N) 0210 - Canonical splice site variant proven to affect splicing of the transcript with a known effect on protein structure. This variant is located in intron 5 of 11 and has been shown to cause skipping of exon 5, resulting in a frameshift deletion and nonsense-mediated decay (NMD) (PMID: 7599635). (P) 0251 - Variant is heterozygous. (N) 0304 - Variant is present in gnomAD <0.01 for a recessive condition (5 heterozygotes, 0 homozygotes). (P) 0701 - Comparable variants have very strong previous evidence for pathogenicity. Other variants predicted to cause NMD have been reported as pathogenic (ClinVar, Decipher). (P) 0801 - Strong previous evidence of pathogenicity in unrelated individuals with severe combined immunodeficiency due to ADA deficiency (ClinVar, PMID: 7599635, PMID: 8673127, PMID: 22968453, PMID: 31858364) . (P) 1002 - Moderate functional evidence supporting abnormal protein function as shown that ADA activity was reduced compared to wild-type and carriers (PMID: 8673127). (P) 1208 - Inheritance information for this variant is not currently available. (N) Legend: (P) - Pathogenic, (N) - Neutral, (B) - Benign (less)
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Pathogenic
(Jul 01, 1996)
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no assertion criteria provided
Method: literature only
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SEVERE COMBINED IMMUNODEFICIENCY, AUTOSOMAL RECESSIVE, T CELL-NEGATIVE, B CELL-NEGATIVE, NK CELL-NEGATIVE, DUE TO ADENOSINE DEAMINASE DEFICIENCY
Affected status: not provided
Allele origin:
germline
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OMIM
Accession: SCV000022213.1
First in ClinVar: Apr 04, 2013 Last updated: Apr 04, 2013 |
Comment on evidence:
In a patient with a mild form of SCID due to ADA deficiency (102700), Hirschhorn et al. (1996) identified compound heterozygosity for 2 mutations in … (more)
In a patient with a mild form of SCID due to ADA deficiency (102700), Hirschhorn et al. (1996) identified compound heterozygosity for 2 mutations in the ADA gene: a G-to-A transition in intron 5, resulting in deletion of exon 5, and R156H (608958.0032). The splice site mutation was inherited from the father and the R156H mutation was inherited from the mother. (less)
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Pathogenic
(Jul 23, 2020)
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no assertion criteria provided
Method: clinical testing
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Severe combined immunodeficiency due to ADA deficiency
Affected status: unknown
Allele origin:
germline
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Natera, Inc.
Accession: SCV002095319.1
First in ClinVar: Apr 23, 2022 Last updated: Apr 23, 2022 |
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Germline Functional Evidence
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 germline classification of this variant
HelpTitle | Author | Journal | Year | Link |
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Chest Radiographs for Distinguishing ADA-SCID from Other Forms of SCID. | Verhagen MV | Journal of clinical immunology | 2020 | PMID: 31858364 |
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 |
Gene therapy for adenosine deaminase-deficient severe combined immune deficiency: clinical comparison of retroviral vectors and treatment plans. | Candotti F | Blood | 2012 | PMID: 22968453 |
Hematopoietic stem cell gene therapy for adenosine deaminase-deficient severe combined immunodeficiency leads to long-term immunological recovery and metabolic correction. | Gaspar HB | Science translational medicine | 2011 | PMID: 21865538 |
Clinical and immunological manifestations of patients with atypical severe combined immunodeficiency. | Felgentreff K | Clinical immunology (Orlando, Fla.) | 2011 | PMID: 21664875 |
Splicing in action: assessing disease causing sequence changes. | Baralle D | Journal of medical genetics | 2005 | PMID: 16199547 |
Spontaneous in vivo reversion to normal of an inherited mutation in a patient with adenosine deaminase deficiency. | Hirschhorn R | Nature genetics | 1996 | PMID: 8673127 |
Four new adenosine deaminase mutations, altering a zinc-binding histidine, two conserved alanines, and a 5' splice site. | Santisteban I | Human mutation | 1995 | PMID: 7599635 |
Text-mined citations for rs761242509 ...
HelpRecord last updated Nov 03, 2024
This date represents the last time this VCV record was updated. The update may be due to an update to one of the included submitted records (SCVs), or due to an update that ClinVar made to the variant such as adding HGVS expressions or a rs number. So this date may be different from the date of the “most recent submission” reported at the top of this page.