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

Germline classification:: Likely pathogenic (1 submission)
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:: RCV000735287.2

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 testicle
Identifiers:: MONDO: MONDO:0009047; MedGen: C0010417; OMIM: 219050; Human Phenotype Ontology: HP:0000028

Name:: Global developmental delay (DD)
Identifiers:: MedGen: C0557874; Human Phenotype Ontology: HP:0001263

Name:: Seizure
Synonyms:: Seizures
Identifiers:: MedGen: C0036572; Human Phenotype Ontology: HP:0001250

Name:: Abnormality of the anterior fontanelle
Identifiers:: MedGen: C4025875; Human Phenotype Ontology: HP:0000236

Name:: Macrocephaly
Synonyms:: Macrocephalus; large head
Identifiers:: MedGen: C2243051; Human Phenotype Ontology: HP:0000256

Name:: Deep plantar creases
Identifiers:: MedGen: C1857953; Human Phenotype Ontology: HP:0001869

Name:: Abnormal cerebral white matter morphology
Synonyms:: Abnormality of the cerebral white matter
Identifiers:: MedGen: C0948163; Human Phenotype Ontology: HP:0002500

Name:: Central hypotonia
Identifiers:: MedGen: C1842364

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000854440	Center for Personalized Medicine, Children's Hospital Los Angeles	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000854440

Center for Personalized Medicine, Children's Hospital Los Angeles

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
Non-Hispanic, White	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical 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 Center for Personalized Medicine, Children's Hospital Los Angeles, SCV000854440.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	Non-Hispanic, White	not provided	not provided	not provided	clinical testing (GTR000552474.2)	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	discovery	(GTR000552474.2)	not provided	not provided	not provided	not provided

Last Updated: May 12, 2024

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