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NM_025114.4(CEP290):c.7220_7223del (p.Lys2407fs) AND multiple conditions

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Dec 13, 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:
RCV001270057.1

Allele description [Variation Report for NM_025114.4(CEP290):c.7220_7223del (p.Lys2407fs)]

NM_025114.4(CEP290):c.7220_7223del (p.Lys2407fs)

Genes:
RLIG1:RNA 5'-phosphate and 3'-OH ligase 1 [Gene - HGNC]
CEP290:centrosomal protein 290 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
12q21.32
Genomic location:
Preferred name:
NM_025114.4(CEP290):c.7220_7223del (p.Lys2407fs)
HGVS:
  • NC_000012.12:g.88049403_88049406del
  • NG_008417.2:g.97813_97816del
  • NM_001009894.3:c.*981_*984delMANE SELECT
  • NM_025114.4:c.7220_7223delMANE SELECT
  • NP_079390.3:p.Lys2407fs
  • LRG_694t1:c.7220_7223del
  • LRG_694:g.97813_97816del
  • LRG_694p1:p.Lys2407fs
  • NC_000012.11:g.88443178_88443181del
  • NC_000012.11:g.88443180_88443183del
  • NG_008417.1:g.97813_97816del
  • NM_025114.3:c.7220_7223del
  • NM_025114.3:c.7220_7223delAGAA
  • NM_025114.4:c.7220_7223delAGAAMANE SELECT
Protein change:
K2407fs
Links:
dbSNP: rs763762899
NCBI 1000 Genomes Browser:
rs763762899
Molecular consequence:
  • NM_001009894.3:c.*981_*984del - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_025114.4:c.7220_7223del - frameshift variant - [Sequence Ontology: SO:0001589]
Observations:
1

Condition(s)

Name:
Global developmental delay (DD)
Identifiers:
MedGen: C0557874; Human Phenotype Ontology: HP:0001263
Name:
Micrognathia
Identifiers:
MedGen: C0025990; Human Phenotype Ontology: HP:0000347
Name:
Abnormal facial shape
Synonyms:
Dysmorphic facies; Dysmorphic facial features
Identifiers:
MedGen: C0424503; Human Phenotype Ontology: HP:0001999
Name:
Hypotonia
Synonyms:
Muscular hypotonia; poor muscle tone
Identifiers:
MedGen: C0026827; Human Phenotype Ontology: HP:0001252

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001448793Knight Diagnostic Laboratories, Oregon Health and Sciences University
criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely pathogenic
(Dec 13, 2019) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknown1not 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 Knight Diagnostic Laboratories, Oregon Health and Sciences University, SCV001448793.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot provided1not providednot providednot provided

Last Updated: Mar 30, 2024