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NM_006565.4(CTCF):c.1342C>T (p.Arg448Ter) AND Intellectual disability-feeding difficulties-developmental delay-microcephaly syndrome

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Aug 14, 2024
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:
RCV004723637.1

Allele description [Variation Report for NM_006565.4(CTCF):c.1342C>T (p.Arg448Ter)]

NM_006565.4(CTCF):c.1342C>T (p.Arg448Ter)

Gene:
CTCF:CCCTC-binding factor [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
16q22.1
Genomic location:
Preferred name:
NM_006565.4(CTCF):c.1342C>T (p.Arg448Ter)
HGVS:
  • NC_000016.10:g.67621576C>T
  • NG_033892.1:g.64170C>T
  • NM_001191022.2:c.358C>T
  • NM_001363916.1:c.1342C>T
  • NM_006565.4:c.1342C>TMANE SELECT
  • NP_001177951.1:p.Arg120Ter
  • NP_001350845.1:p.Arg448Ter
  • NP_006556.1:p.Arg448Ter
  • NC_000016.9:g.67655479C>T
Protein change:
R120*
Molecular consequence:
  • NM_001191022.2:c.358C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001363916.1:c.1342C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_006565.4:c.1342C>T - nonsense - [Sequence Ontology: SO:0001587]
Observations:
1

Condition(s)

Name:
Intellectual disability-feeding difficulties-developmental delay-microcephaly syndrome (MRD21)
Synonyms:
INTELLECTUAL DEVELOPMENTAL DISORDER, AUTOSOMAL DOMINANT 21
Identifiers:
MONDO: MONDO:0014213; MedGen: C3809686; Orphanet: 363611; OMIM: 615502

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV005326519Diagnostics Services (NGS), CSIR - Centre For Cellular And Molecular Biology
criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely pathogenic
(Aug 14, 2024) 		unknownclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownyes11not 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 Diagnostics Services (NGS), CSIR - Centre For Cellular And Molecular Biology, SCV005326519.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (1)

Description

The c.1342C>T variant is not present in publicly available population databases like 1000 Genomes, EVS, Indian Exome Database or our in-house exome database. This variant is present in ExAC and gnomAD at low frequencies. This variant has been previously reported in an individual with nodular medulloblastoma [PMID: 30419952]. In-silico pathogenicity prediction programs like MutationTaster2021, CADD, Franklin, Varsome etc predicted this variant to be likely deleterious. This variant creates a premature translational stop signal at the 448th amino acid position of the wild-type transcript that may either result in translation of a truncated protein or cause nonsense mediated decay of the mRNA. This variant is located in a mutational hotspot region of the gene and a missense variant in the same position (Arg448Gln) has been previously reported in patients affected with neurodevelopmental disorders [PMID: 31239556, 33004838].

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providednot provided1not provided1not provided

Last Updated: Nov 18, 2024