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NM_031448.6(C19orf12):c.161G>T (p.Gly54Val) AND not provided

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Oct 1, 2018
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:
RCV000486662.3

Allele description [Variation Report for NM_031448.6(C19orf12):c.161G>T (p.Gly54Val)]

NM_031448.6(C19orf12):c.161G>T (p.Gly54Val)

Gene:
C19orf12:chromosome 19 open reading frame 12 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
19q12
Genomic location:
Preferred name:
NM_031448.6(C19orf12):c.161G>T (p.Gly54Val)
HGVS:
  • NC_000019.10:g.29702977C>A
  • NG_031970.2:g.17813G>T
  • NM_001031726.4:c.161G>T
  • NM_001256046.3:c.161G>T
  • NM_001256047.2:c.161G>T
  • NM_001282929.1:c.-32G>T
  • NM_001282930.3:c.-32G>T
  • NM_001282931.3:c.-32G>T
  • NM_031448.6:c.161G>TMANE SELECT
  • NP_001026896.2:p.Gly65Val
  • NP_001026896.3:p.Gly54Val
  • NP_001242975.1:p.Gly54Val
  • NP_001242976.1:p.Gly54Val
  • NP_113636.2:p.Gly54Val
  • NC_000019.9:g.30193884C>A
  • NM_001031726.3:c.194G>T
  • NM_031448.4:c.161G>T
Protein change:
G54V
Links:
dbSNP: rs752450983
NCBI 1000 Genomes Browser:
rs752450983
Molecular consequence:
  • NM_001282929.1:c.-32G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001282930.3:c.-32G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001282931.3:c.-32G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001031726.4:c.161G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001256046.3:c.161G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001256047.2:c.161G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_031448.6:c.161G>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000573899GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Likely pathogenic
(Oct 1, 2018) 		germlineclinical testing

Citation Link

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Summary from all submissions

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

Details of each submission

From GeneDx, SCV000573899.4

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

Description

The c.194 G>T variant in the C19orf12 gene has been previously reported in the homozygous state, and in the presence of a loss of function C19orf12 variant, in two unrelated sets of affected siblings with mitochondrial membrane protein-associated neurodegeneration (MPAN) (Hogarth et al., 2013; Yoganathan et al., 2016). This variant is not observed at a significant frequency in large population cohorts (Lek et al., 2016). In-silico splice prediction models predict that c.194 G>T may weaken the natural splice acceptor site for intron 2. However, in the absence of RNA/functional studies, the effect of the c.194 G>T change in this individual is unknown. If c.194 G>T does not alter splicing, it will result in the G65V missense change. The G65V variant is a conservative amino acid substitution, which is not likely to impact secondary protein structure as these residues share similar properties. This substitution occurs at a position within a transmembrane domain that is conserved across species, and in silico analysis predicts this variant is probably damaging to the protein structure/function. We interpret the c.194 G>T variant as a likely pathogenic variant.

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

Last Updated: Oct 8, 2024