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NM_001367721.1(CASK):c.1504-97G>A AND Syndromic X-linked intellectual disability Najm type

Germline classification:
Likely benign (1 submission)
Last evaluated:
Jul 29, 2021
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:
RCV003330242.2

Allele description [Variation Report for NM_001367721.1(CASK):c.1504-97G>A]

NM_001367721.1(CASK):c.1504-97G>A

Gene:
CASK:calcium/calmodulin dependent serine protein kinase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Xp11.4
Genomic location:
Preferred name:
NM_001367721.1(CASK):c.1504-97G>A
HGVS:
  • NC_000023.11:g.41569843C>T
  • NG_016754.2:g.358192G>A
  • NM_001126054.3:c.1504-97G>A
  • NM_001126055.3:c.1486-97G>A
  • NM_001367721.1:c.1504-97G>AMANE SELECT
  • NM_001410745.1:c.1486-97G>A
  • NM_003688.4:c.1504-97G>A
  • NC_000023.10:g.41429096C>T
Molecular consequence:
  • NM_001126054.3:c.1504-97G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001126055.3:c.1486-97G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001367721.1:c.1504-97G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001410745.1:c.1486-97G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_003688.4:c.1504-97G>A - intron variant - [Sequence Ontology: SO:0001627]
Observations:
1

Condition(s)

Name:
Syndromic X-linked intellectual disability Najm type (MICPCH)
Synonyms:
MICPCH SYNDROME; Mental retardation and microcephaly with pontine and cerebellar hypoplasia; MENTAL RETARDATION, X-LINKED, SYNDROMIC, NAJM TYPE; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0010417; MedGen: C2677903; Orphanet: 163937; OMIM: 300749

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004037269Dr. med. U. Finckh, Human Genetics, Eurofins MVZ
criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely benign
(Jul 29, 2021) 		paternalclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedpaternalno21not 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 Dr. med. U. Finckh, Human Genetics, Eurofins MVZ, SCV004037269.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided2not providednot providedclinical testing PubMed (1)

Description

The variant is not present in gnomAD. Splice prediction suggest the creation of a cryptic splice donor site. Detected in a female proband with epilepsy and developmental delay, and subsequently in her unaffected father. The variant thus is classified as likely benign.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1paternalnonot providednot providednot provided2not provided1not provided

Last Updated: Oct 7, 2023