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NM_004606.5(TAF1):c.3992T>A (p.Ile1331Asn) AND Intellectual disability, X-linked, syndromic 33

Germline classification:
Uncertain significance (2 submissions)
Last evaluated:
Feb 14, 2020
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
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:
RCV001027756.3

Allele description [Variation Report for NM_004606.5(TAF1):c.3992T>A (p.Ile1331Asn)]

NM_004606.5(TAF1):c.3992T>A (p.Ile1331Asn)

Gene:
TAF1:TATA-box binding protein associated factor 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Xq13.1
Genomic location:
Preferred name:
NM_004606.5(TAF1):c.3992T>A (p.Ile1331Asn)
HGVS:
  • NC_000023.11:g.71401733T>A
  • NG_012771.2:g.40470T>A
  • NM_001286074.2:c.3992T>A
  • NM_004606.5:c.3992T>AMANE SELECT
  • NM_138923.4:c.3929T>A
  • NP_001273003.2:p.Ile1331Asn
  • NP_004597.2:p.Ile1351Asn
  • NP_004597.3:p.Ile1331Asn
  • NP_620278.2:p.Ile1310Asn
  • NC_000023.10:g.70621583T>A
  • NM_004606.4:c.4052T>A
  • NR_104387.2:n.4010T>A
  • NR_104388.2:n.4010T>A
  • NR_104389.2:n.4010T>A
  • NR_104390.2:n.4010T>A
  • NR_104391.2:n.4010T>A
  • NR_104392.2:n.4010T>A
  • NR_104393.2:n.4010T>A
  • NR_104394.2:n.4010T>A
  • NR_104395.2:n.4010T>A
Protein change:
I1310N
Links:
dbSNP: rs1602549992
NCBI 1000 Genomes Browser:
rs1602549992
Molecular consequence:
  • NM_001286074.2:c.3992T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_004606.5:c.3992T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_138923.4:c.3929T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NR_104387.2:n.4010T>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_104388.2:n.4010T>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_104389.2:n.4010T>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_104390.2:n.4010T>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_104391.2:n.4010T>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_104392.2:n.4010T>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_104393.2:n.4010T>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_104394.2:n.4010T>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_104395.2:n.4010T>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:
Intellectual disability, X-linked, syndromic 33 (MRXS33)
Synonyms:
INTELLECTUAL DEVELOPMENTAL DISORDER, X-LINKED, SYNDROMIC 33
Identifiers:
MONDO: MONDO:0010500; MedGen: C4225418; OMIM: 300966

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000998774Genome Medicine, Institute for Basic Research in Developmental Disabilities
no assertion criteria provided
Uncertain significance
(Sep 23, 2019) 		maternalclinical testing

SCV001768725Gene Discovery Core-Manton Center, Boston Children's Hospital
no assertion criteria provided
Uncertain significance
(Feb 14, 2020) 		germlineresearch

Help

Summary from all submissions

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

Details of each submission

From Genome Medicine, Institute for Basic Research in Developmental Disabilities, SCV000998774.1

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

From Gene Discovery Core-Manton Center, Boston Children's Hospital, SCV001768725.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedresearchnot provided

Description

This variant is interpretted as Pathogenic for MRXS33 intellectual disability syndrome; X-linked recessive. PM1 - Located in a mutational hot spot and/or critical and well-established functional domain without benign variation. PM2 - Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium. PP2 - Missense variant in a gene that has a low rate of benign missense variation and in which missense variants are a common mechanism of disease.

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

Last Updated: Aug 5, 2023