NM_001379110.1(SLC9A6):c.1662-19_1662-3del AND multiple conditions

Clinical significance:Likely pathogenic

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000735325.1

Allele description [Variation Report for NM_001379110.1(SLC9A6):c.1662-19_1662-3del]

NM_001379110.1(SLC9A6):c.1662-19_1662-3del

Gene:
SLC9A6:solute carrier family 9 member A6 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
Xq26.3
Genomic location:
Preferred name:
NM_001379110.1(SLC9A6):c.1662-19_1662-3del
HGVS:
  • NC_000023.11:g.136040057_136040073del
  • NG_017160.1:g.59631_59647del
  • NM_001042537.2:c.1728-19_1728-3del
  • NM_001177651.2:c.1572-19_1572-3del
  • NM_001330652.2:c.1476-19_1476-3del
  • NM_001379110.1:c.1662-19_1662-3delMANE SELECT
  • NM_006359.3:c.1632-19_1632-3del
  • NC_000023.10:g.135122216_135122232del
  • NM_001042537.1:c.1728-19_1728-3delTCTTCCTTAACCACCGC
Links:
dbSNP: rs1569525894
NCBI 1000 Genomes Browser:
rs1569525894
Molecular consequence:
  • NM_001042537.2:c.1728-19_1728-3del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001177651.2:c.1572-19_1572-3del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001330652.2:c.1476-19_1476-3del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001379110.1:c.1662-19_1662-3del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_006359.3:c.1632-19_1632-3del - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:
Autistic disorder of childhood onset (AUTS)
Identifiers:
MONDO: MONDO:0005260; MedGen: C0004352; OMIM: 209850; Human Phenotype Ontology: HP:0000717
Name:
Pectus excavatum
Synonyms:
Funnel chest
Identifiers:
MONDO: MONDO:0008213; MedGen: C2051831; OMIM: 169300; Human Phenotype Ontology: HP:0000767
Name:
Esotropia
Synonyms:
Convergent strabismus; Inward turning cross eyed
Identifiers:
MONDO: MONDO:0004896; MedGen: C0014877; Human Phenotype Ontology: HP:0000565
Name:
Global developmental delay (DD)
Synonyms:
Cognitive delay; Delayed cognitive development; Delayed development; See all synonyms [MedGen]
Identifiers:
MedGen: C0557874; Human Phenotype Ontology: HP:0001263
Name:
Seizures
Identifiers:
MedGen: C0036572; Human Phenotype Ontology: HP:0001250
Name:
Short stature
Synonyms:
Decreased body height; Height less than 3rd percentile; Small stature; See all synonyms [MedGen]
Identifiers:
MedGen: C0349588; Human Phenotype Ontology: HP:0004322
Name:
Failure to thrive
Synonyms:
Postnatal failure to thrive; Poor weight gain; Weight faltering; See all synonyms [MedGen]
Identifiers:
MedGen: C2315100; Human Phenotype Ontology: HP:0001508
Name:
Deeply set eye
Synonyms:
Deep set eye; Deep-set eyes; Enophthalmos; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0001210; MedGen: C0423224; Human Phenotype Ontology: HP:0000490
Name:
Clinodactyly of the 5th finger
Synonyms:
Bilateral fifth digit clinodactyly; Bilateral fifth finger clinodactyly; Clinodactyly of fifth digit; See all synonyms [MedGen]
Identifiers:
MedGen: C1850049; Human Phenotype Ontology: HP:0004209
Name:
Impaired use of nonverbal behaviors
Synonyms:
Impaired use of nonverbal behaviours
Identifiers:
MedGen: C4021798; Human Phenotype Ontology: HP:0000758
Name:
Generalized hypotonia
Synonyms:
Generalized muscular hypotonia; Decreased muscle tone; Low muscle tone
Identifiers:
MedGen: C1858120; Human Phenotype Ontology: HP:0001290
Name:
Chorea
Synonyms:
Choreatic disease; Choreic movements; Choreiform movements
Identifiers:
MONDO: MONDO:0001595; MedGen: C0008489; Human Phenotype Ontology: HP:0002072
Name:
Postnatal microcephaly
Synonyms:
Deceleration of head growth; Postnatal deceleration of head circumference; Acquired microcephaly; See all synonyms [MedGen]
Identifiers:
MedGen: C0431352; Human Phenotype Ontology: HP:0005484
Name:
Focal white matter lesions
Identifiers:
MedGen: C4024946; Human Phenotype Ontology: HP:0007042

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000854479CHLA Center for Personalized Medicine,Children's Hospital, Los Angelescriteria provided, single submitter
Likely pathogenicgermlineclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From CHLA Center for Personalized Medicine,Children's Hospital, Los Angeles, SCV000854479.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing
(GTR000552474.2)
PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot provideddiscovery
(GTR000552474.2)
not providednot providednot providednot provided

Last Updated: Oct 25, 2021

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