NM_000489.6(ATRX):c.3913A>C (p.Lys1305Gln) AND Alpha thalassemia-X-linked intellectual disability syndrome

Germline classification:: Benign (2 submissions)
Last evaluated:: Jan 22, 2024
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:: RCV000863037.17

Allele description [Variation Report for NM_000489.6(ATRX):c.3913A>C (p.Lys1305Gln)]

NM_000489.6(ATRX):c.3913A>C (p.Lys1305Gln)

Gene:

ATRX:ATRX chromatin remodeler [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

Xq21.1

Genomic location:

Preferred name:

NM_000489.6(ATRX):c.3913A>C (p.Lys1305Gln)

HGVS:

NC_000023.11:g.77664675T>G
NG_008838.3:g.126595A>C
NM_000489.6:c.3913A>CMANE SELECT
NM_138270.5:c.3799A>C
NP_000480.3:p.Lys1305Gln
NP_000480.3:p.Lys1305Gln
NP_612114.2:p.Lys1267Gln
LRG_1153t1:c.3913A>C
LRG_1153:g.126595A>C
LRG_1153p1:p.Lys1305Gln
NC_000023.10:g.76920164T>G
NM_000489.3:c.3913A>C
NM_000489.4:c.3913A>C
NM_000489.5:c.3913A>C

Protein change:

K1267Q

Links:

dbSNP: rs782708557

NCBI 1000 Genomes Browser:

rs782708557

Molecular consequence:

NM_000489.6:c.3913A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_138270.5:c.3799A>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Alpha thalassemia-X-linked intellectual disability syndrome (ATRX)
Synonyms:: ALPHA-THALASSEMIA/MENTAL RETARDATION SYNDROME, X-LINKED; ATR, NONDELETION TYPE; ATR-X syndrome; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0010519; MedGen: C1845055; Orphanet: 847; OMIM: 301040

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001003629	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Benign (Jan 22, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001453022	Natera, Inc.	no assertion criteria provided	Likely benign (Jun 3, 2020)	germline	clinical testing

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001003629

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Benign
(Jan 22, 2024)

germline

clinical testing

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

SCV001453022

Natera, Inc.

no assertion criteria provided

Likely benign
(Jun 3, 2020)

germline

clinical testing

Help

Summary from all submissions

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

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group, Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001003629.6

#	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 Natera, Inc., SCV001453022.1

#	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	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Jan 13, 2025

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