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NM_006306.4(SMC1A):c.1977del (p.Lys660fs) AND Abnormality of the nervous system

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Jul 10, 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:
RCV001814493.1

Allele description [Variation Report for NM_006306.4(SMC1A):c.1977del (p.Lys660fs)]

NM_006306.4(SMC1A):c.1977del (p.Lys660fs)

Gene:
SMC1A:structural maintenance of chromosomes 1A [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
Xp11.22
Genomic location:
Preferred name:
NM_006306.4(SMC1A):c.1977del (p.Lys660fs)
HGVS:
  • NC_000023.11:g.53405326del
  • NG_006988.2:g.22345del
  • NM_001281463.1:c.1911del
  • NM_006306.4:c.1977delMANE SELECT
  • NP_001268392.1:p.Lys638fs
  • NP_006297.2:p.Lys660fs
  • LRG_773t1:c.1911del
  • LRG_773:g.22345del
  • LRG_773p1:p.Lys638fs
  • NC_000023.10:g.53432258del
  • NM_006306.4:c.1977delGMANE SELECT
Protein change:
K638fs
Links:
dbSNP: rs2146599602
NCBI 1000 Genomes Browser:
rs2146599602
Molecular consequence:
  • NM_001281463.1:c.1911del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_006306.4:c.1977del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:
Abnormality of the nervous system
Synonyms:
Congenital nervous system disorder
Identifiers:
MONDO: MONDO:0002320; MedGen: C0497552; Human Phenotype Ontology: HP:0000707

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001755466Kariminejad - Najmabadi Pathology & Genetics Center
criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely pathogenic
(Jul 10, 2021) 		de novoclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedde novoyesnot providednot 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 Kariminejad - Najmabadi Pathology & Genetics Center, SCV001755466.1

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

Last Updated: Dec 24, 2023