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NM_003119.4(SPG7):c.2280G>A (p.Pro760=) AND Hereditary spastic paraplegia 7

Germline classification:
Benign/Likely benign (3 submissions)
Last evaluated:
Jan 28, 2024
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:
RCV001000211.26

Allele description [Variation Report for NM_003119.4(SPG7):c.2280G>A (p.Pro760=)]

NM_003119.4(SPG7):c.2280G>A (p.Pro760=)

Gene:
SPG7:SPG7 matrix AAA peptidase subunit, paraplegin [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
16q24.3
Genomic location:
Preferred name:
NM_003119.4(SPG7):c.2280G>A (p.Pro760=)
Other names:
p.P760P:CCG>CCA
HGVS:
  • NC_000016.10:g.89556985G>A
  • NG_008082.1:g.53589G>A
  • NM_001363850.1:c.*58G>A
  • NM_003119.4:c.2280G>AMANE SELECT
  • NP_003110.1:p.Pro760=
  • NC_000016.9:g.89623393G>A
  • NM_003119.2:c.2280G>A
  • NM_003119.3:c.2280G>A
  • NM_199367.1:c.*20075G>A
Links:
dbSNP: rs11559075
NCBI 1000 Genomes Browser:
rs11559075
Molecular consequence:
  • NM_001363850.1:c.*58G>A - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_003119.4:c.2280G>A - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Name:
Hereditary spastic paraplegia 7 (SPG7)
Synonyms:
Spastic paraplegia 7; Hereditary spastic paraplegia Paraplegin type; Autosomal recessive spastic paraplegia type 7
Identifiers:
MONDO: MONDO:0011803; MedGen: C1846564; Orphanet: 99013; OMIM: 607259

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000287874Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Benign
(Jan 28, 2024)
germlineclinical testing

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

SCV000399768Illumina Laboratory Services, Illumina
criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)
Likely benign
(Jan 13, 2018)
germlineclinical testing

Citation Link,

SCV001156719ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
criteria provided, single submitter

(ARUP Molecular Germline Variant Investigation Process 2024)
Benign
(Nov 29, 2023)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV000287874.9

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

From Illumina Laboratory Services, Illumina, SCV000399768.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories, SCV001156719.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Jul 23, 2024