NM_032018.7(SPRTN):c.718_718+3del AND not provided

Germline classification:: Pathogenic (2 submissions)
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:: RCV000210757.4

Allele description [Variation Report for NM_032018.7(SPRTN):c.718_718+3del]

NM_032018.7(SPRTN):c.718_718+3del

Gene:

SPRTN:SprT-like N-terminal domain [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

1q42.2

Genomic location:

Preferred name:

NM_032018.7(SPRTN):c.718_718+3del

HGVS:

NC_000001.11:g.231351571_231351574del
NG_042052.1:g.18636_18639del
NM_001010984.4:c.718_721del
NM_001261462.3:c.589_592del
NM_032018.7:c.718_718+3delMANE SELECT
NP_001010984.1:p.Gly240fs
NP_001248391.1:p.Gly197fs
NC_000001.10:g.231487317_231487320del
NM_032018.5:c.717_718+2delAGGT

Protein change:

G197fs

Links:

OMIM: 616086.0002; dbSNP: rs587593493

NCBI 1000 Genomes Browser:

rs587593493

Molecular consequence:

NM_001010984.4:c.718_721del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001261462.3:c.589_592del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_032018.7:c.718_718+3del - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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Corynebacterium amycolatum ICIS 9
Corynebacterium amycolatum ICIS 9

biosample
2-(4-chlorophenoxy)-N-(4-(2-(4-chlorophenoxy)acetamido)cyclohexyl)acetamide [Sup...
2-(4-chlorophenoxy)-N-(4-(2-(4-chlorophenoxy)acetamido)cyclohexyl)acetamide [Supplementary Concept]
a nootropic agent; structure in first source<br/>Date introduced: July 1, 2015<br/>

MeSH
C000599093 (1)
MeSH

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000188639	Neurogenetics Research; Murdoch Childrens Research Institute	criteria provided, single submitter (Submitter's publication)	pathogenic	germline	not provided	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000188639

Neurogenetics Research; Murdoch Childrens Research Institute

criteria provided, single submitter

(Submitter's publication)

pathogenic

germline

not provided

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

Description

Autosomal recessive atypical progeroid syndrome with hepatic cellular carcinoma. Heterozygous mutation in 1 family: SCV000188639

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	not provided	not provided	not provided	not provided	2	not provided	literature only

Citations

PubMed

Mutations in SPRTN cause early onset hepatocellular carcinoma, genomic instability and progeroid features.

Lessel D, Vaz B, Halder S, Lockhart PJ, Marinovic-Terzic I, Lopez-Mosqueda J, Philipp M, Sim JC, Smith KR, Oehler J, Cabrera E, Freire R, Pope K, Nahid A, Norris F, Leventer RJ, Delatycki MB, Barbi G, von Ameln S, Högel J, Degoricija M, Fertig R, et al.

Nat Genet. 2014 Nov;46(11):1239-44. doi: 10.1038/ng.3103. Epub 2014 Sep 28.

PubMed [citation]

PMID:: 25261934
PMCID:: PMC4343211

Details of each submission

From Neurogenetics Research; Murdoch Childrens Research Institute, SCV000188611.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	not provided	PubMed (1)

Description

Converted during submission to Pathogenic.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	not provided	1	not provided	not provided		not provided	not provided	not provided	not provided

From Neurogenetics Research; Murdoch Childrens Research Institute, SCV000188639.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	not provided	PubMed (1)

Description

Converted during submission to Pathogenic.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	not provided	1	not provided	not provided		not provided	not provided	not provided	not provided

Flagged submissions

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000188611	Neurogenetics Research; Murdoch Childrens Research Institute	flagged submission Reason: This record appears to be redundant with a more recent record from the same submitter. Notes: SCV000188611 appears to be redundant with SCV000188639. (Submitter's publication)	pathogenic	germline	not provided	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000188611

Neurogenetics Research; Murdoch Childrens Research Institute

flagged submission

Reason: This record appears to be redundant with a more recent record from the same submitter.

Notes: SCV000188611 appears to be redundant with SCV000188639.

(Submitter's publication)

pathogenic

germline

not provided

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

Last Updated: May 7, 2024

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Relating variation to medicine