NM_022893.4(BCL11A):c.143G>T (p.Cys48Phe) AND Dias-Logan syndrome

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Oct 17, 2022
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:: RCV000240280.5

Allele description [Variation Report for NM_022893.4(BCL11A):c.143G>T (p.Cys48Phe)]

NM_022893.4(BCL11A):c.143G>T (p.Cys48Phe)

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.143G>T (p.Cys48Phe)

HGVS:

NC_000002.12:g.60546213C>A
NG_011968.1:g.12286G>T
NM_001363864.1:c.143G>T
NM_001365609.1:c.143G>T
NM_018014.4:c.143G>T
NM_022893.4:c.143G>TMANE SELECT
NM_138559.2:c.143G>T
NP_001350793.1:p.Cys48Phe
NP_001352538.1:p.Cys48Phe
NP_060484.2:p.Cys48Phe
NP_075044.2:p.Cys48Phe
NP_612569.1:p.Cys48Phe
NC_000002.11:g.60773348C>A
NM_022893.3:c.143G>T
Q9H165:p.Cys48Phe

Protein change:

C48F; CYS48PHE

Links:

UniProtKB: Q9H165#VAR_076922; OMIM: 606557.0002; dbSNP: rs886037865

NCBI 1000 Genomes Browser:

rs886037865

Molecular consequence:

NM_001363864.1:c.143G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001365609.1:c.143G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_018014.4:c.143G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_022893.4:c.143G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_138559.2:c.143G>T - missense variant - [Sequence Ontology: SO:0001583]

Observations:

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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000298226	OMIM	no assertion criteria provided	Pathogenic (Sep 8, 2016)	germline	literature only	PubMed (1) [See all records that cite this PMID]
SCV002583595	Centre for Inherited Metabolic Diseases, Karolinska University Hospital	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Oct 17, 2022)	de novo	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000298226

OMIM

no assertion criteria provided

Pathogenic
(Sep 8, 2016)

germline

literature only

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

SCV002583595

Centre for Inherited Metabolic Diseases, Karolinska University Hospital

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Oct 17, 2022)

de novo

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	de novo	yes	1	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	not provided	not provided	not provided	not provided	not provided	not provided	literature only

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

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 OMIM, SCV000298226.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	literature only	PubMed (1)

Description

In a boy with intellectual developmental disorder with persistence of fetal hemoglobin (617101), Dias et al. (2016) identified a de novo heterozygous c.143G-T transversion (c.143G-T, NM_022893.3) in exon 2 of the BCL11A gene, resulting in a cys48-to-phe (C48F) substitution in the N-terminal region. The mutation was found by exome sequencing.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	not provided	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Centre for Inherited Metabolic Diseases, Karolinska University Hospital, SCV002583595.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1		1	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	de novo	yes	not provided	not provided	not provided		1	not provided	not provided	not provided

Last Updated: Apr 30, 2023

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