NM_004187.5(KDM5C):c.2243+1G>T AND Syndromic X-linked intellectual disability Claes-Jensen type

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Jul 9, 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:
RCV001078174.2

Allele description [Variation Report for NM_004187.5(KDM5C):c.2243+1G>T]

NM_004187.5(KDM5C):c.2243+1G>T

Gene:
KDM5C:lysine demethylase 5C [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Xp11.22
Genomic location:
Preferred name:
NM_004187.5(KDM5C):c.2243+1G>T
HGVS:
  • NC_000023.11:g.53198976C>A
  • NG_008085.2:g.31447G>T
  • NM_001146702.2:c.2042+1G>T
  • NM_001282622.3:c.2240+1G>T
  • NM_001353978.3:c.2243+1G>T
  • NM_001353979.2:c.2240+1G>T
  • NM_001353981.2:c.2243+1G>T
  • NM_001353982.2:c.2240+1G>T
  • NM_001353984.2:c.2243+1G>T
  • NM_004187.5:c.2243+1G>TMANE SELECT
  • NC_000023.10:g.53228158C>A
  • NM_004187.3:c.2243+1G>T
Links:
dbSNP: rs2073058023
NCBI 1000 Genomes Browser:
rs2073058023
Molecular consequence:
  • NM_001146702.2:c.2042+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001282622.3:c.2240+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001353978.3:c.2243+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001353979.2:c.2240+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001353981.2:c.2243+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001353982.2:c.2240+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001353984.2:c.2243+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_004187.5:c.2243+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
Functional consequence:
sequence_variant_affecting_splicing [Sequence Ontology: SO:1000071]
Observations:
1

Condition(s)

Name:
Syndromic X-linked intellectual disability Claes-Jensen type (MRXSCJ)
Synonyms:
INTELLECTUAL DEVELOPMENTAL DISORDER, X-LINKED, SYNDROMIC, CLAES-JENSEN TYPE
Identifiers:
MONDO: MONDO:0010355; MedGen: C1845243; Orphanet: 85279; OMIM: 300534

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001190370Breda Genetics srl
criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely pathogenic
(Jul 9, 2019) 		maternalclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedmaternalyes1not providednot 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 Breda Genetics srl, SCV001190370.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
11not providednot providedclinical testing PubMed (1)

Description

The variant affects the donor splice site of intron 15 and is therefore highly likely to impact the splicing process by causing the retention of the following intron and the formation of an aberrant mRNA, which is unlikely to be exported and translated into protein. This variant has not been reported in dbSNP, gnomAD, 1000 Genomes, NHLI Exome Sequencing Project (ESP) or ClinVar. Pathogenic splicing variants have already been reported in literature (PMID: 18697827, 25644381).

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

Last Updated: Aug 5, 2023