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NM_022893.4(BCL11A):c.317C>T (p.Thr106Met) AND Dias-Logan syndrome

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Oct 18, 2019
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:
RCV001249751.4

Allele description [Variation Report for NM_022893.4(BCL11A):c.317C>T (p.Thr106Met)]

NM_022893.4(BCL11A):c.317C>T (p.Thr106Met)

Gene:
BCL11A:BCL11 transcription factor A [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
2p16.1
Genomic location:
Preferred name:
NM_022893.4(BCL11A):c.317C>T (p.Thr106Met)
HGVS:
  • NC_000002.12:g.60546039G>A
  • NG_011968.1:g.12460C>T
  • NM_001363864.1:c.317C>T
  • NM_001365609.1:c.317C>T
  • NM_018014.4:c.317C>T
  • NM_022893.4:c.317C>TMANE SELECT
  • NM_138559.2:c.317C>T
  • NP_001350793.1:p.Thr106Met
  • NP_001352538.1:p.Thr106Met
  • NP_060484.2:p.Thr106Met
  • NP_075044.2:p.Thr106Met
  • NP_612569.1:p.Thr106Met
  • NC_000002.11:g.60773174G>A
  • NM_022893.3:c.317C>T
Protein change:
T106M
Links:
dbSNP: rs1670134440
NCBI 1000 Genomes Browser:
rs1670134440
Molecular consequence:
  • NM_001363864.1:c.317C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001365609.1:c.317C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_018014.4:c.317C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_022893.4:c.317C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_138559.2:c.317C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Dias-Logan syndrome
Synonyms:
INTELLECTUAL DEVELOPMENTAL DISORDER WITH HEREDITARY PERSISTENCE OF FETAL HEMOGLOBIN; Intellectual developmental disorder with persistence of fetal hemoglobin
Identifiers:
MONDO: MONDO:0014914; MedGen: C4310833; OMIM: 617101

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001423784Illumina Laboratory Services, Illumina
criteria provided, single submitter

(ICSLVariantClassificationCriteria RUGD 01 April 2020)		Uncertain significance
(Oct 18, 2019) 		unknownclinical testing

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

Citation Link

Help

Summary from all submissions

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

Citations

PubMed

BCL11A Haploinsufficiency Causes an Intellectual Disability Syndrome and Dysregulates Transcription.

Dias C, Estruch SB, Graham SA, McRae J, Sawiak SJ, Hurst JA, Joss SK, Holder SE, Morton JE, Turner C, Thevenon J, Mellul K, Sánchez-Andrade G, Ibarra-Soria X, Deriziotis P, Santos RF, Lee SC, Faivre L, Kleefstra T, Liu P, Hurles ME; DDD Study., et al.

Am J Hum Genet. 2016 Aug 4;99(2):253-74. doi: 10.1016/j.ajhg.2016.05.030. Epub 2016 Jul 21.

PubMed [citation]
PMID:
27453576
PMCID:
PMC4974071

Identification of novel mutations in the HbF repressor gene BCL11A in patients with autism and intelligence disabilities.

Cai T, Chen X, Li J, Xiang B, Yang L, Liu Y, Chen Q, He Z, Sun K, Liu PP.

Am J Hematol. 2017 Dec;92(12):E653-E656. doi: 10.1002/ajh.24902. Epub 2017 Sep 28. No abstract available.

PubMed [citation]
PMID:
28891213

Details of each submission

From Illumina Laboratory Services, Illumina, SCV001423784.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

The BCL11A c.317C>T (p.Thr106Met) variant is a missense variant. A literature search was performed for the gene, cDNA change, and amino acid change. No publications were found based on this search. This variant is absent from the Genome Aggregation Database in a region of good sequencing coverage. It is therefore presumed to be rare. The p.Thr106Met variant occurs in exon 2 of BCL11A, within an N-terminal region involved in dimerization of BCL11A isoforms and the interaction with chromatin remodeling complexes. Pathogenic missense variants have been reported in this region and shown to disrupt BCL11A localization, dimerization, and transcriptional regulatory activity (Dias et al. 2016), but missense variants in this region are also found in ostensibly healthy individuals (Genome Aggregation Database; Cai et al. 2017). Based on the limited evidence, the p.Thr106Met variant is classified as a variant of of unknown significance for BCL11A-related intellectual disability.

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

Last Updated: Apr 9, 2023