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NM_001166114.2(PNPLA6):c.3823G>A (p.Ala1275Thr) AND Hereditary spastic paraplegia 39

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Mar 10, 2022
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:
RCV001917957.6

Allele description [Variation Report for NM_001166114.2(PNPLA6):c.3823G>A (p.Ala1275Thr)]

NM_001166114.2(PNPLA6):c.3823G>A (p.Ala1275Thr)

Gene:
PNPLA6:patatin like phospholipase domain containing 6 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
19p13.2
Genomic location:
Preferred name:
NM_001166114.2(PNPLA6):c.3823G>A (p.Ala1275Thr)
HGVS:
  • NC_000019.10:g.7561020G>A
  • NG_013374.1:g.31869G>A
  • NM_001166111.2:c.3853G>A
  • NM_001166112.2:c.3628G>A
  • NM_001166113.1:c.3709G>A
  • NM_001166114.2:c.3823G>AMANE SELECT
  • NM_006702.5:c.3709G>A
  • NP_001159583.1:p.Ala1285Thr
  • NP_001159584.1:p.Ala1210Thr
  • NP_001159585.1:p.Ala1237Thr
  • NP_001159586.1:p.Ala1275Thr
  • NP_006693.3:p.Ala1237Thr
  • NC_000019.9:g.7625906G>A
Protein change:
A1210T
Links:
dbSNP: rs139102273
NCBI 1000 Genomes Browser:
rs139102273
Molecular consequence:
  • NM_001166111.2:c.3853G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001166112.2:c.3628G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001166113.1:c.3709G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001166114.2:c.3823G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_006702.5:c.3709G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Hereditary spastic paraplegia 39 (SPG39)
Synonyms:
SPASTIC PARAPLEGIA 39, AUTOSOMAL RECESSIVE; Spastic paraplegia 39; NTE related motor neuron disorder
Identifiers:
MONDO: MONDO:0012787; MedGen: C2677586; Orphanet: 139480; OMIM: 612020

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002168762Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Mar 10, 2022) 		germlineclinical testing

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

Help

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 Labcorp Genetics (formerly Invitae), Labcorp, SCV002168762.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The threonine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. This variant has not been reported in the literature in individuals affected with PNPLA6-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces alanine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 1237 of the PNPLA6 protein (p.Ala1237Thr).

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

Last Updated: Sep 29, 2024