NM_003119.4(SPG7):c.1617del (p.Val540fs) AND not provided

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Sep 1, 2017
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000256054.17

Allele description [Variation Report for NM_003119.4(SPG7):c.1617del (p.Val540fs)]

NM_003119.4(SPG7):c.1617del (p.Val540fs)

Gene:

SPG7:SPG7 matrix AAA peptidase subunit, paraplegin [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

16q24.3

Genomic location:

Preferred name:

NM_003119.4(SPG7):c.1617del (p.Val540fs)

HGVS:

NC_000016.10:g.89548067del
NG_008082.1:g.44671del
NM_001363850.1:c.1617del
NM_003119.4:c.1617delMANE SELECT
NP_001350779.1:p.Val540fs
NP_003110.1:p.Val540fs
NC_000016.9:g.89614474del
NC_000016.9:g.89614475del
NM_003119.2:c.1617delC
NM_003119.3:c.1617delC

Protein change:

V540fs

Links:

OMIM: 602783.0008; dbSNP: rs762795756

NCBI 1000 Genomes Browser:

rs762795756

Molecular consequence:

NM_001363850.1:c.1617del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_003119.4:c.1617del - frameshift variant - [Sequence Ontology: SO:0001589]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000322297	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Pathogenic (Aug 25, 2016)	germline	clinical testing	Citation Link,
SCV001246897	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Pathogenic (Sep 1, 2017)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000322297

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Pathogenic
(Aug 25, 2016)

germline

clinical testing

Citation Link,

SCV001246897

CeGaT Center for Human Genetics Tuebingen

criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)

Pathogenic
(Sep 1, 2017)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	1	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From GeneDx, SCV000322297.6

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

The c.1617delC variant in the SPG7 gene has been reported previously in association with hereditary spastic paraplegia in an individual who was homozygous for c.1617delC and an individual who was heterozygous for c.1617delC and a large deletion of the SPG7 gene (Arnoldi et al., 2008; Orsucci et al., 2014). The deletion causes a frameshift starting with codon Valine 540, changes this amino acid to a Cysteine residue and creates a premature Stop codon at position 52 of the new reading frame, denoted p.Val540CysfsX52. This pathogenic variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay.

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

From CeGaT Center for Human Genetics Tuebingen, SCV001246897.20

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	not provided	clinical testing	not provided

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

Last Updated: Apr 15, 2024

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