NM_006886.4(ATP5F1E):c.85A>G (p.Thr29Ala) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Feb 11, 2023
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:: RCV003834752.2

Allele description [Variation Report for NM_006886.4(ATP5F1E):c.85A>G (p.Thr29Ala)]

NM_006886.4(ATP5F1E):c.85A>G (p.Thr29Ala)

Genes:

ATP5F1E:ATP synthase F1 subunit epsilon [Gene - OMIM - HGNC]
SLMO2-ATP5E:SLMO2-ATP5E readthrough [Gene]

Variant type:

single nucleotide variant

Cytogenetic location:

20q13.32

Genomic location:

Preferred name:

NM_006886.4(ATP5F1E):c.85A>G (p.Thr29Ala)

HGVS:

NC_000020.11:g.59030377T>C
NG_031871.2:g.6991A>G
NM_001001977.1:c.85A>G
NM_006886.4:c.85A>GMANE SELECT
NP_001001977.1:p.Thr29Ala
NP_008817.1:p.Thr29Ala
NP_008817.1:p.Thr29Ala
NC_000020.10:g.57605432T>C
NM_006886.3:c.85A>G
NR_037929.1:n.789A>G
NR_037930.1:n.530A>G

Protein change:

T29A

Molecular consequence:

NM_001001977.1:c.85A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_006886.4:c.85A>G - missense variant - [Sequence Ontology: SO:0001583]
NR_037929.1:n.789A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_037930.1:n.530A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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band 4.1-like protein 3 isoform X34 [Gorilla gorilla gorilla]
band 4.1-like protein 3 isoform X34 [Gorilla gorilla gorilla]
gi|2493371678|ref|XP_055224463.1|

Protein
PREDICTED: Gorilla gorilla gorilla erythrocyte membrane protein band 4.1 like 3 ...
PREDICTED: Gorilla gorilla gorilla erythrocyte membrane protein band 4.1 like 3 (EPB41L3), transcript variant X6, mRNA
gi|2694955547|ref|XM_063699429.1|

Nucleotide
band 4.1-like protein 3 isoform X35 [Gorilla gorilla gorilla]
band 4.1-like protein 3 isoform X35 [Gorilla gorilla gorilla]
gi|2493371680|ref|XP_055224464.1|

Protein
myomegalin isoform 17 [Homo sapiens]
myomegalin isoform 17 [Homo sapiens]
gi|2056392262|ref|NP_001382227.1|

Protein
txid9792[Organism:noexp] (173)
PMC

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004640042	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Feb 11, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004640042

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Feb 11, 2023)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical 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, SCV004640042.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical 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 alanine 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 ATP5E-related conditions. This variant is present in population databases (rs750526513, gnomAD 0.002%). This sequence change replaces threonine, which is neutral and polar, with alanine, which is neutral and non-polar, at codon 29 of the ATP5E protein (p.Thr29Ala).

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

Last Updated: Sep 29, 2024

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