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NM_001385875.1(ZFYVE27):c.290C>T (p.Ala97Val) AND Spastic paraplegia

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Nov 5, 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:
RCV002805838.3

Allele description [Variation Report for NM_001385875.1(ZFYVE27):c.290C>T (p.Ala97Val)]

NM_001385875.1(ZFYVE27):c.290C>T (p.Ala97Val)

Gene:
ZFYVE27:zinc finger FYVE-type containing 27 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
10q24.2
Genomic location:
Preferred name:
NM_001385875.1(ZFYVE27):c.290C>T (p.Ala97Val)
HGVS:
  • NC_000010.11:g.97744750C>T
  • NG_017075.1:g.12630C>T
  • NM_001002261.4:c.290C>T
  • NM_001002262.4:c.290C>T
  • NM_001174119.2:c.194C>T
  • NM_001174120.2:c.198-3519C>T
  • NM_001174121.2:c.-5C>T
  • NM_001174122.2:c.198-4724C>T
  • NM_001385871.1:c.290C>T
  • NM_001385875.1:c.290C>TMANE SELECT
  • NM_001385876.1:c.329C>T
  • NM_001385877.1:c.290C>T
  • NM_001385878.1:c.290C>T
  • NM_001385879.1:c.290C>T
  • NM_001385880.1:c.290C>T
  • NM_001385881.1:c.269-15C>T
  • NM_001385882.1:c.290C>T
  • NM_001385883.1:c.290C>T
  • NM_001385884.1:c.290C>T
  • NM_001385885.1:c.194C>T
  • NM_001385886.1:c.290C>T
  • NM_001385887.1:c.194C>T
  • NM_001385888.1:c.194C>T
  • NM_001385889.1:c.290C>T
  • NM_001385890.1:c.86C>T
  • NM_001385891.1:c.86C>T
  • NM_001385892.1:c.86C>T
  • NM_001385893.1:c.86C>T
  • NM_001385894.1:c.86C>T
  • NM_001385895.1:c.86C>T
  • NM_001385896.1:c.86C>T
  • NM_001385897.1:c.86C>T
  • NM_001385898.1:c.86C>T
  • NM_001385899.1:c.53C>T
  • NM_001385900.1:c.53C>T
  • NM_001385901.1:c.198-3519C>T
  • NM_001385902.1:c.198-3519C>T
  • NM_001385903.1:c.53C>T
  • NM_001385904.1:c.53C>T
  • NM_001385905.1:c.53C>T
  • NM_001385906.1:c.198-3519C>T
  • NM_001385908.1:c.198-3519C>T
  • NM_001385911.1:c.198-3519C>T
  • NM_001385915.1:c.-5C>T
  • NM_001385916.1:c.53C>T
  • NM_001385917.1:c.53C>T
  • NM_001385918.1:c.198-4724C>T
  • NM_001385919.1:c.32-5581C>T
  • NM_144588.7:c.290C>T
  • NP_001002261.1:p.Ala97Val
  • NP_001002262.1:p.Ala97Val
  • NP_001167590.1:p.Ala65Val
  • NP_001372800.1:p.Ala97Val
  • NP_001372804.1:p.Ala97Val
  • NP_001372805.1:p.Ala110Val
  • NP_001372806.1:p.Ala97Val
  • NP_001372807.1:p.Ala97Val
  • NP_001372808.1:p.Ala97Val
  • NP_001372809.1:p.Ala97Val
  • NP_001372811.1:p.Ala97Val
  • NP_001372812.1:p.Ala97Val
  • NP_001372813.1:p.Ala97Val
  • NP_001372814.1:p.Ala65Val
  • NP_001372815.1:p.Ala97Val
  • NP_001372816.1:p.Ala65Val
  • NP_001372817.1:p.Ala65Val
  • NP_001372818.1:p.Ala97Val
  • NP_001372819.1:p.Ala29Val
  • NP_001372820.1:p.Ala29Val
  • NP_001372821.1:p.Ala29Val
  • NP_001372822.1:p.Ala29Val
  • NP_001372823.1:p.Ala29Val
  • NP_001372824.1:p.Ala29Val
  • NP_001372825.1:p.Ala29Val
  • NP_001372826.1:p.Ala29Val
  • NP_001372827.1:p.Ala29Val
  • NP_001372828.1:p.Ala18Val
  • NP_001372829.1:p.Ala18Val
  • NP_001372832.1:p.Ala18Val
  • NP_001372833.1:p.Ala18Val
  • NP_001372834.1:p.Ala18Val
  • NP_001372845.1:p.Ala18Val
  • NP_001372846.1:p.Ala18Val
  • NP_653189.3:p.Ala97Val
  • NC_000010.10:g.99504507C>T
  • NM_001002261.3:c.290C>T
  • NR_169794.1:n.460C>T
  • NR_169795.1:n.418C>T
  • NR_169796.1:n.485C>T
  • NR_169797.1:n.460C>T
  • NR_169798.1:n.460C>T
  • NR_169800.1:n.485C>T
  • NR_169801.1:n.485C>T
  • NR_169803.1:n.460C>T
  • NR_169804.1:n.489C>T
  • NR_169805.1:n.489C>T
  • NR_169806.1:n.485C>T
  • NR_169808.1:n.528C>T
  • NR_169809.1:n.414C>T
  • NR_169810.1:n.485C>T
  • NR_169811.1:n.460C>T
Protein change:
A110V
Molecular consequence:
  • NM_001174121.2:c.-5C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001385915.1:c.-5C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001174120.2:c.198-3519C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001174122.2:c.198-4724C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001385881.1:c.269-15C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001385901.1:c.198-3519C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001385902.1:c.198-3519C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001385906.1:c.198-3519C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001385908.1:c.198-3519C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001385911.1:c.198-3519C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001385918.1:c.198-4724C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001385919.1:c.32-5581C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001002261.4:c.290C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001002262.4:c.290C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001174119.2:c.194C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001385871.1:c.290C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001385875.1:c.290C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001385876.1:c.329C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001385877.1:c.290C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001385878.1:c.290C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001385879.1:c.290C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001385880.1:c.290C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001385882.1:c.290C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001385883.1:c.290C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001385884.1:c.290C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001385885.1:c.194C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001385886.1:c.290C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001385887.1:c.194C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001385888.1:c.194C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001385889.1:c.290C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001385890.1:c.86C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001385891.1:c.86C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001385892.1:c.86C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001385893.1:c.86C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001385894.1:c.86C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001385895.1:c.86C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001385896.1:c.86C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001385897.1:c.86C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001385898.1:c.86C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001385899.1:c.53C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001385900.1:c.53C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001385903.1:c.53C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001385904.1:c.53C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001385905.1:c.53C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001385916.1:c.53C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001385917.1:c.53C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_144588.7:c.290C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NR_169794.1:n.460C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_169795.1:n.418C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_169796.1:n.485C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_169797.1:n.460C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_169798.1:n.460C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_169800.1:n.485C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_169801.1:n.485C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_169803.1:n.460C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_169804.1:n.489C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_169805.1:n.489C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_169806.1:n.485C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_169808.1:n.528C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_169809.1:n.414C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_169810.1:n.485C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_169811.1:n.460C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:
Spastic paraplegia
Identifiers:
MedGen: C0037772; Human Phenotype Ontology: HP:0001258

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003030248Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Nov 5, 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, SCV003030248.2

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

Description

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. 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 valine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. This variant has not been reported in the literature in individuals affected with ZFYVE27-related conditions. This variant is present in population databases (rs367545791, gnomAD 0.004%). This sequence change replaces alanine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 97 of the ZFYVE27 protein (p.Ala97Val).

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

Last Updated: Nov 24, 2024