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NM_004380.3(CREBBP):c.5558A>C (p.Gln1853Pro) AND Menke-Hennekam syndrome 1

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Aug 25, 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:
RCV002280359.2

Allele description [Variation Report for NM_004380.3(CREBBP):c.5558A>C (p.Gln1853Pro)]

NM_004380.3(CREBBP):c.5558A>C (p.Gln1853Pro)

Gene:
CREBBP:CREB binding protein [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
16p13.3
Genomic location:
Preferred name:
NM_004380.3(CREBBP):c.5558A>C (p.Gln1853Pro)
Other names:
NM_004380.3:c.5558A>C
HGVS:
  • NC_000016.10:g.3729489T>G
  • NG_009873.2:g.156225A>C
  • NM_001079846.1:c.5444A>C
  • NM_004380.2:c.5558A>C
  • NM_004380.3:c.5558A>CMANE SELECT
  • NP_001073315.1:p.Gln1815Pro
  • NP_004371.2:p.Gln1853Pro
  • LRG_1426t1:c.5558A>C
  • LRG_1426:g.156225A>C
  • LRG_1426p1:p.Gln1853Pro
  • NC_000016.9:g.3779490T>G
Protein change:
Q1815P
Molecular consequence:
  • NM_001079846.1:c.5444A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_004380.3:c.5558A>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Menke-Hennekam syndrome 1 (MKHK1)
Identifiers:
MONDO: MONDO:0020763; MedGen: C5193034; OMIM: 618332

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV002568397Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely pathogenic
(Aug 25, 2022)
germlinecuration

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedcuration

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 Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard, SCV002568397.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcuration PubMed (1)

Description

The heterozygous p.Gln1853Pro variant in CREBBP was identified in 1 individual with a neurodevelopmental disorder including delayed speech and language development, global developmental delay, intellectual disability, abnormal social behavior, hearing impairment, and abnormal facial shape via a collaborative study between the Broad Institute's Center for Mendelian Genomics and the Neurodev Study (https://www.neurodevproject.org/). Trio exome analysis showed this variant to be de novo. The p.Gln1853Pro variant in CREBBP has not been previously reported in individuals with Menke-Hennekam or Rubinstein-Taybi syndrome and was absent from large population studies. Computational prediction tools and conservation analyses suggest that this variant may impact the protein, though this information is not predictive enough to determine pathogenicity. The number of missense variants reported in CREBBP in the general population is lower than expected, suggesting there is little benign variation in this gene and slightly increasing the possibility that a missense variant in this gene may not be tolerated. In summary, although additional studies are required to fully establish its clinical significance, this variant is likely pathogenic for autosomal dominant CREBBP-related disorder. ACMG/AMP Criteria applied: PS2_Moderate, PP3_Moderate, PM2_supporting, PP2 (Richards 2015).

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

Last Updated: May 1, 2024