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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 stars
criteria provided, multiple submitters, no conflicts
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:
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
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)

Name:
Intellectual disability-strabismus syndrome (NEDBGF)
Synonyms:
NEURODEVELOPMENTAL DISORDER WITH BRAIN ABNORMALITIES, POOR GROWTH, AND DYSMORPHIC FACIES
Identifiers:
MONDO: MONDO:0014119; MedGen: C4750838; Orphanet: 363528; OMIM: 615286

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000082799OMIM
no assertion criteria provided
Pathogenic
(Jul 1, 2013)
germlineliterature only

PubMed (3)
[See all records that cite these PMIDs]

SCV000196407Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center
no assertion criteria provided

(research)
Likely pathogenic
(Dec 1, 2014)
germlineresearch

PubMed (1)
[See all records that cite this PMID]

SCV000786718Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard - Broad Institute Center for Mendelian Genomics (CMG)
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenicgermlineresearch

PubMed (1)
[See all records that cite this PMID]

SCV000996290Pathology and Clinical Laboratory Medicine, King Fahad Medical City
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenicgermlineclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV001132975Biochemical Molecular Genetic Laboratory, King Abdulaziz Medical City
no assertion criteria provided
Pathogenic
(Aug 25, 2019)
germlineclinical testing

SCV001156076Section for Clinical Neurogenetics, University of Tübingen
no assertion criteria provided
Pathogenic
(Aug 1, 2019)
germlineresearch

PubMed (2)
[See all records that cite these PMIDs]

SCV001426529Centogene AG - the Rare Disease Company
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenicgermlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

SCV001521996Baylor Genetics
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Jun 3, 2020)
unknownclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV001547514Department of Biochemistry, Faculty of Medicine, University of Khartoum
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Mar 25, 2021)
germlineresearch

PubMed (3)
[See all records that cite these PMIDs]

SCV002022276Revvity Omics, Revvity
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Jul 6, 2022)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV004099517Hadassah Hebrew University Medical Center
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely pathogenicgermlineclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV004171164Institute of Human Genetics, University Hospital of Duesseldorf
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenicgermlinenot provided

PubMed (1)
[See all records that cite this PMID]

SCV004804796Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely pathogenic
(Mar 17, 2024)
germlineresearch

PubMed (1)
[See all records that cite this PMID]

SCV005088727Breakthrough Genomics, Breakthrough Genomics
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Jun 23, 2021)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes2not providednot providednot providednot providedclinical testing, research, not provided
not providedunknownyesnot providednot providednot providednot providednot providedclinical testing
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing, research
Arabgermlineyes11not providednot providednot providednot providedclinical testing
Unspecifiedgermlineyesnot provided1not providednot providednot providedresearch

Citations

PubMed

A new case confirming and expanding the phenotype spectrum of ADAT3-related intellectual disability syndrome.

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.

PubMed [citation]
PMID:
30296593

Accelerating novel candidate gene discovery in neurogenetic disorders via whole-exome sequencing of prescreened multiplex consanguineous families.

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.

PubMed [citation]
PMID:
25558065
See all PubMed Citations (7)

Details of each submission

From OMIM, SCV000082799.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature 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.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot providednot providednot providednot providednot provided

From Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, SCV000196407.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedresearch PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard - Broad Institute Center for Mendelian Genomics (CMG), SCV000786718.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1Unspecifiednot providednot providednot providedresearch 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.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot provided1not provided

From Pathology and Clinical Laboratory Medicine, King Fahad Medical City, SCV000996290.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1Arab11not providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided11not providednot providednot provided

From Biochemical Molecular Genetic Laboratory, King Abdulaziz Medical City, SCV001132975.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Section for Clinical Neurogenetics, University of Tübingen, SCV001156076.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedresearch PubMed (2)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Centogene AG - the Rare Disease Company, SCV001426529.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Baylor Genetics, SCV001521996.1

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

Description

This variant was determined to be pathogenic according to ACMG Guidelines, 2015 [PMID:25741868].

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providednot providednot providednot providednot providednot provided

From Department of Biochemistry, Faculty of Medicine, University of Khartoum, SCV001547514.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided2not providednot providedresearch 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).

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided2not providednot providednot provided

From Revvity Omics, Revvity, SCV002022276.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Hadassah Hebrew University Medical Center, SCV004099517.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Institute of Human Genetics, University Hospital of Duesseldorf, SCV004171164.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providednot provided PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, SCV004804796.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedresearch PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Breakthrough Genomics, Breakthrough Genomics, SCV005088727.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical 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].

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 1, 2024