NM_138422.4(ADAT3):c.430G>A (p.Val144Met) AND Intellectual disability-strabismus syndrome
- Germline classification:
- Pathogenic/Likely pathogenic (14 submissions)
- Last evaluated:
- Mar 17, 2024
- Review status:
- 2 stars out of maximum of 4 starscriteria provided, multiple submitters, no conflicts
- Somatic classification
of clinical impact: - None
- Review status:
- (0/4) 0 stars out of maximum of 4 starsno assertion criteria provided
- Somatic classification
of oncogenicity: - None
- Review status:
- (0/4) 0 stars out of maximum of 4 starsno assertion criteria provided
- Record status:
- current
- Accession:
- RCV000162122.22
Allele description [Variation Report for NM_138422.4(ADAT3):c.430G>A (p.Val144Met)]
NM_138422.4(ADAT3):c.430G>A (p.Val144Met)
- Genes:
- ADAT3:adenosine deaminase tRNA specific 3 [Gene - OMIM - HGNC]
SCAMP4:secretory carrier membrane protein 4 [Gene - OMIM - HGNC] - Variant type:
- single nucleotide variant
- Cytogenetic location:
- 19p13.3
- Genomic location:
- Preferred name:
- NM_138422.4(ADAT3):c.430G>A (p.Val144Met)
- HGVS:
- NC_000019.10:g.1912477G>A
- NG_051211.1:g.12264G>A
- NM_001329533.2:c.382G>A
- NM_001329539.2:c.-125-5217G>A
- NM_001329540.2:c.-41-2502G>A
- NM_079834.4:c.-41-2502G>AMANE SELECT
- NM_138422.4:c.430G>AMANE SELECT
- NP_001316462.1:p.Val128Met
- NP_612431.2:p.Val144Met
- NC_000019.9:g.1912476G>A
- NM_001329533.1:c.382G>A
- NM_138422.1:c.382G>A
- NM_138422.2:c.430G>A
- NM_138422.3:c.430G>A
This HGVS expression did not pass validation- Protein change:
- V128M; VAL128MET
- Links:
- OMIM: 615302.0001; dbSNP: rs730882213
- NCBI 1000 Genomes Browser:
- rs730882213
- Molecular consequence:
- NM_001329539.2:c.-125-5217G>A - intron variant - [Sequence Ontology: SO:0001627]
- NM_001329540.2:c.-41-2502G>A - intron variant - [Sequence Ontology: SO:0001627]
- NM_079834.4:c.-41-2502G>A - intron variant - [Sequence Ontology: SO:0001627]
- NM_001329533.2:c.382G>A - missense variant - [Sequence Ontology: SO:0001583]
- NM_138422.4:c.430G>A - missense variant - [Sequence Ontology: SO:0001583]
- Observations:
- 11
Condition(s)
Assertion and evidence details
Submission Accession | Submitter | Review Status (Assertion method) | Clinical Significance (Last evaluated) | Origin | Method | Citations |
---|---|---|---|---|---|---|
SCV000082799 | OMIM | no assertion criteria provided | Pathogenic (Jul 1, 2013) | germline | literature only | |
SCV000196407 | Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center | no assertion criteria provided (research) | Likely pathogenic (Dec 1, 2014) | germline | research | |
SCV000786718 | Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard - Broad Institute Center for Mendelian Genomics (CMG) | criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic | germline | research | |
SCV000996290 | Pathology and Clinical Laboratory Medicine, King Fahad Medical City | criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic | germline | clinical testing | |
SCV001132975 | Biochemical Molecular Genetic Laboratory, King Abdulaziz Medical City | no assertion criteria provided | Pathogenic (Aug 25, 2019) | germline | clinical testing | |
SCV001156076 | Section for Clinical Neurogenetics, University of Tübingen | no assertion criteria provided | Pathogenic (Aug 1, 2019) | germline | research | |
SCV001426529 | Centogene AG - the Rare Disease Company | criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic | germline | clinical testing | |
SCV001521996 | Baylor Genetics | criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic (Jun 3, 2020) | unknown | clinical testing | |
SCV001547514 | Department of Biochemistry, Faculty of Medicine, University of Khartoum | criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic (Mar 25, 2021) | germline | research | |
SCV002022276 | Revvity Omics, Revvity | criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic (Jul 6, 2022) | germline | clinical testing | |
SCV004099517 | Hadassah Hebrew University Medical Center | criteria provided, single submitter (ACMG Guidelines, 2015) | Likely pathogenic | germline | clinical testing | |
SCV004171164 | Institute of Human Genetics, University Hospital of Duesseldorf | criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic | germline | not provided | |
SCV004804796 | Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center | criteria provided, single submitter (ACMG Guidelines, 2015) | Likely pathogenic (Mar 17, 2024) | germline | research | |
SCV005088727 | Breakthrough Genomics, Breakthrough Genomics | criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic (Jun 23, 2021) | germline | clinical testing |
Summary from all submissions
Ethnicity | Origin | Affected | Individuals | Families | Chromosomes tested | Number Tested | Family history | Method |
---|---|---|---|---|---|---|---|---|
not provided | germline | yes | 2 | not provided | not provided | not provided | not provided | clinical testing, research, not provided |
not provided | unknown | yes | not provided | not provided | not provided | not provided | not provided | clinical testing |
not provided | germline | not provided | not provided | not provided | not provided | not provided | not provided | literature only |
not provided | germline | unknown | not provided | not provided | not provided | not provided | not provided | clinical testing, research |
Arab | germline | yes | 11 | not provided | not provided | not provided | not provided | clinical testing |
Unspecified | germline | yes | not provided | 1 | not provided | not provided | not provided | research |
Citations
PubMed
Sharkia R, Zalan A, Jabareen-Masri A, Zahalka H, Mahajnah M.
Eur J Med Genet. 2019 Nov;62(11):103549. doi: 10.1016/j.ejmg.2018.10.001. Epub 2018 Oct 6.
- PMID:
- 30296593
Alazami AM, Patel N, Shamseldin HE, Anazi S, Al-Dosari MS, Alzahrani F, Hijazi H, Alshammari M, Aldahmesh MA, Salih MA, Faqeih E, Alhashem A, Bashiri FA, Al-Owain M, Kentab AY, Sogaty S, Al Tala S, Temsah MH, Tulbah M, Aljelaify RF, Alshahwan SA, Seidahmed MZ, et al.
Cell Rep. 2015 Jan 13;10(2):148-61. doi: 10.1016/j.celrep.2014.12.015. Epub 2014 Dec 31.
- PMID:
- 25558065
Details of each submission
From OMIM, SCV000082799.4
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | literature only | PubMed (3) |
Description
In affected members of 8 consanguineous Arab families with neurodevelopmental disorder with brain abnormalities, poor growth, and dysmorphic facies (NEDBGF; 615286) Alazami et al. (2013) identified a homozygous c.382G-A transition in the ADAT3 gene, resulting in a val128-to-met (V128M) substitution at a highly conserved residue. Molecular modeling indicated that the mutation occurs in a hook that protrudes from the surface of the protein and would disrupt this protrusion. The mutation, which was found by homozygosity mapping and exome sequencing and confirmed by Sanger sequencing, segregated with the disorder in all families and was not found in several large control exome databases or in 580 ethnically matched alleles. Haplotype analysis indicated a founder effect, which was estimated to have occurred between 65 and 111 generations ago. Most of the patients also had esotropia and failure to thrive; some had microcephaly and mild brain malformations on MRI.
In 15 affected members of 11 apparently unrelated Arab families with NEDBGF, El-Hattab et al. (2016) identified homozygosity for the same V128M founder mutation in the ADAT3 gene. El-Hattab et al. (2016) noted that all but 1 of the families with this mutation were from Saudi Arabia.
Sharkia et al. (2019) identified a homozygous V128M mutation in 2 sibs, born of consanguineous Arab parents, with NEDBGF. The mutation, which was found by whole-exome sequencing and confirmed by Sanger sequencing, segregated with the disorder in the family. Functional studies of the variant and studies of patient cells were not performed.
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | not provided | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, SCV000196407.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | research | PubMed (1) |
# | 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 |
From Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard - Broad Institute Center for Mendelian Genomics (CMG), SCV000786718.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | Unspecified | not provided | not provided | not provided | research | PubMed (1) |
Description
The homozgous p.Val144Met variant was identified by our study in one individual with mental retardation. Of note, a first cousin who was noted to also have mental retardation was a carrier for this variant. The p.Val144Met variant is believed to be pathogenic based on numberous reports by other laboratories in the literature and databases.
# | 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 | 1 | not provided |
From Pathology and Clinical Laboratory Medicine, King Fahad Medical City, SCV000996290.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | Arab | 11 | not provided | not provided | clinical testing | PubMed (1) |
# | 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 | 11 | not provided | not provided | not provided |
From Biochemical Molecular Genetic Laboratory, King Abdulaziz Medical City, SCV001132975.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | not provided |
# | 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 |
From Section for Clinical Neurogenetics, University of Tübingen, SCV001156076.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | research | PubMed (2) |
# | 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 |
From Centogene AG - the Rare Disease Company, SCV001426529.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | PubMed (2) |
# | 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 |
From Baylor Genetics, SCV001521996.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | PubMed (1) |
Description
This variant was determined to be pathogenic according to ACMG Guidelines, 2015 [PMID:25741868].
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | unknown | yes | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Department of Biochemistry, Faculty of Medicine, University of Khartoum, SCV001547514.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | 2 | not provided | not provided | research | PubMed (3) |
Description
We detected the variant NM_138422.3(ADAT3): c.430G>A (p.Val144Met, rs730882213) in two female siblings with Mental retardation, autosomal recessive 36 using whole-exome sequencing. We validated the variant's status in the patients using Sanger sequencing and detected it in a heterozygous status in their parents. Multiple reports previously classified the variant NM_138422.3(ADAT3): c.430G>A (p.Val144Met, rs730882213) as pathogenic (Alazami et al., 2013; El-Hattab et al., 2016).
# | 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 | 2 | not provided | not provided | not provided |
From Revvity Omics, Revvity, SCV002022276.3
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | PubMed (1) |
# | 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 |
From Hadassah Hebrew University Medical Center, SCV004099517.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | PubMed (1) |
# | 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 |
From Institute of Human Genetics, University Hospital of Duesseldorf, SCV004171164.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | not provided | PubMed (1) |
# | 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 |
From Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, SCV004804796.2
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | research | PubMed (1) |
# | 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 |
From Breakthrough Genomics, Breakthrough Genomics, SCV005088727.2
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | PubMed (1) |
Description
This variant is predicted to be damaging by in-silico missense prediction tools (SIFT and Polyphen2). The variant (also known as V128M in literature) was previously reported in patients with intellectual disability and considered as founder mutation in the Saudi Arabian population [PMID: 26842963, 23620220, 32214227]. Functional studies using cell lines derived from intellectual disability-affected individuals showed a severe reduction in tRNA deaminase activity [PMID: 31263000].
# | 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: Sep 1, 2024