NM_024996.7(GFM1):c.455A>C (p.Gln152Pro) AND not provided

Germline classification:
Conflicting interpretations of pathogenicity (2 submissions)
Last evaluated:
Nov 4, 2021
Review status:
criteria provided, conflicting classifications
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:
RCV000658473.6

Allele description [Variation Report for NM_024996.7(GFM1):c.455A>C (p.Gln152Pro)]

NM_024996.7(GFM1):c.455A>C (p.Gln152Pro)

Gene:
GFM1:G elongation factor mitochondrial 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
3q25.32
Genomic location:
Preferred name:
NM_024996.7(GFM1):c.455A>C (p.Gln152Pro)
HGVS:
  • NC_000003.12:g.158646830A>C
  • NG_008441.1:g.7303A>C
  • NM_001308164.2:c.455A>C
  • NM_001308166.2:c.455A>C
  • NM_001374355.1:c.455A>C
  • NM_001374356.1:c.455A>C
  • NM_001374357.1:c.230A>C
  • NM_001374358.1:c.234+1049A>C
  • NM_001374359.1:c.5+1049A>C
  • NM_001374360.1:c.5+1049A>C
  • NM_001374361.1:c.5+1049A>C
  • NM_024996.7:c.455A>CMANE SELECT
  • NP_001295093.1:p.Gln152Pro
  • NP_001295095.1:p.Gln152Pro
  • NP_001361284.1:p.Gln152Pro
  • NP_001361285.1:p.Gln152Pro
  • NP_001361286.1:p.Gln77Pro
  • NP_079272.4:p.Gln152Pro
  • NP_079272.4:p.Gln152Pro
  • NC_000003.11:g.158364619A>C
  • NM_024996.5:c.455A>C
  • NR_164499.1:n.563A>C
  • NR_164500.1:n.563A>C
  • NR_164502.1:n.563A>C
Protein change:
Q152P
Links:
dbSNP: rs780319278
NCBI 1000 Genomes Browser:
rs780319278
Molecular consequence:
  • NM_001374358.1:c.234+1049A>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001374359.1:c.5+1049A>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001374360.1:c.5+1049A>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001374361.1:c.5+1049A>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001308164.2:c.455A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001308166.2:c.455A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001374355.1:c.455A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001374356.1:c.455A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001374357.1:c.230A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_024996.7:c.455A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NR_164499.1:n.563A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_164500.1:n.563A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_164502.1:n.563A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000780245GeneDx
criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)		Likely pathogenic
(May 29, 2019) 		germlineclinical testing

Citation Link,

SCV002190157Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Nov 4, 2021) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
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 GeneDx, SCV000780245.3

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

Description

Has not been previously published as pathogenic or benign to our knowledge; Not observed at a significant frequency in large population cohorts (Lek et al., 2016); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect

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

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002190157.2

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

Description

This sequence change replaces glutamine, which is neutral and polar, with proline, which is neutral and non-polar, at codon 152 of the GFM1 protein (p.Gln152Pro). This variant is present in population databases (rs780319278, gnomAD 0.002%). This variant has not been reported in the literature in individuals affected with GFM1-related conditions. ClinVar contains an entry for this variant (Variation ID: 546574). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt GFM1 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.

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

Last Updated: Sep 29, 2024