NM_001365999.1(SZT2):c.6120_6122del (p.Val2041del) AND multiple conditions

Clinical significance:Likely pathogenic

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000735287.1

Allele description [Variation Report for NM_001365999.1(SZT2):c.6120_6122del (p.Val2041del)]

NM_001365999.1(SZT2):c.6120_6122del (p.Val2041del)

Gene:
SZT2:SZT2 subunit of KICSTOR complex [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
1p34.2
Genomic location:
Preferred name:
NM_001365999.1(SZT2):c.6120_6122del (p.Val2041del)
HGVS:
  • NC_000001.11:g.43437256_43437258del
  • NG_029091.1:g.52372_52374del
  • NM_001365999.1:c.6120_6122delMANE SELECT
  • NM_015284.4:c.5949_5951del
  • NP_001352928.1:p.Val2041del
  • NP_056099.3:p.Val1984del
  • NC_000001.10:g.43902925_43902927del
  • NC_000001.10:g.43902927_43902929del
  • NM_015284.3:c.5949_5951del
  • NM_015284.3:c.5949_5951delTGT
  • p.Val1984del
Protein change:
V1984del
Links:
dbSNP: rs746200792
NCBI 1000 Genomes Browser:
rs746200792
Molecular consequence:
  • NM_001365999.1:c.6120_6122del - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_015284.4:c.5949_5951del - inframe_deletion - [Sequence Ontology: SO:0001822]

Condition(s)

Name:
Cryptorchidism
Synonyms:
Cryptorchidism, unilateral or bilateral; Undescended testes; Undescended testis; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0009047; MedGen: C0010417; OMIM: 219050; Human Phenotype Ontology: HP:0000028
Name:
Global developmental delay (DD)
Synonyms:
Cognitive delay; Delayed cognitive development; Delayed development; See all synonyms [MedGen]
Identifiers:
MedGen: C0557874; Human Phenotype Ontology: HP:0001263
Name:
Seizures
Identifiers:
MedGen: C0036572; Human Phenotype Ontology: HP:0001250
Name:
Abnormality of the anterior fontanelle
Synonyms:
Abnormality of the forehead soft spot
Identifiers:
MedGen: C4025875; Human Phenotype Ontology: HP:0000236
Name:
Macrocephalus
Synonyms:
Macrocephaly; Large head circumference; Macrocrania; See all synonyms [MedGen]
Identifiers:
MedGen: C2243051; Human Phenotype Ontology: HP:0000256
Name:
Deep plantar creases
Identifiers:
MedGen: C1857953; Human Phenotype Ontology: HP:0001869
Name:
Abnormality of the cerebral white matter
Synonyms:
Abnormality of subcortical white matter; Cerebral white matter abnormalities; White matter abnormalities; See all synonyms [MedGen]
Identifiers:
MedGen: C0948163; Human Phenotype Ontology: HP:0002500
Name:
Central hypotonia
Identifiers:
MedGen: C1842364; Human Phenotype Ontology: HP:0011398

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000854440CHLA Center for Personalized Medicine,Children's Hospital, Los Angelescriteria provided, single submitter
Likely pathogenicgermlineclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
Non-Hispanic, Whitegermlineyesnot 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 CHLA Center for Personalized Medicine,Children's Hospital, Los Angeles, SCV000854440.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1Non-Hispanic, Whitenot providednot providednot providedclinical testing
(GTR000552474.2)
PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot provideddiscovery
(GTR000552474.2)
not providednot providednot providednot provided

Last Updated: Apr 12, 2021

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