NM_031448.6(C19orf12):c.83C>T (p.Ser28Phe) AND not specified

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Mar 20, 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:: RCV002239978.2

Allele description [Variation Report for NM_031448.6(C19orf12):c.83C>T (p.Ser28Phe)]

NM_031448.6(C19orf12):c.83C>T (p.Ser28Phe)

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.83C>T (p.Ser28Phe)

HGVS:

NC_000019.10:g.29708331G>A
NG_031970.2:g.12459C>T
NM_001031726.4:c.83C>T
NM_001256046.3:c.83C>T
NM_001256047.2:c.83C>T
NM_001282929.1:c.-32-5354C>T
NM_001282930.3:c.-32-5354C>T
NM_001282931.3:c.-231C>T
NM_031448.6:c.83C>TMANE SELECT
NP_001026896.3:p.Ser28Phe
NP_001242975.1:p.Ser28Phe
NP_001242976.1:p.Ser28Phe
NP_113636.2:p.Ser28Phe
NC_000019.9:g.30199238G>A
NM_001031726.3:c.116C>T

Protein change:

S28F

Links:

dbSNP: rs1204865094

NCBI 1000 Genomes Browser:

rs1204865094

Molecular consequence:

NM_001282931.3:c.-231C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001282929.1:c.-32-5354C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001282930.3:c.-32-5354C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001031726.4:c.83C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001256046.3:c.83C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001256047.2:c.83C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_031448.6:c.83C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002511576	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Uncertain significance (Mar 20, 2023)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 31087512, 23269600 Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002511576

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Uncertain significance
(Mar 20, 2023)

germline

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

Citation Link

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

Autosomal dominant mitochondrial membrane protein-associated neurodegeneration (MPAN).

Gregory A, Lotia M, Jeong SY, Fox R, Zhen D, Sanford L, Hamada J, Jahic A, Beetz C, Freed A, Kurian MA, Cullup T, van der Weijden MCM, Nguyen V, Setthavongsack N, Garcia D, Krajbich V, Pham T, Woltjer R, George BP, Minks KQ, Paciorkowski AR, et al.

Mol Genet Genomic Med. 2019 Jul;7(7):e00736. doi: 10.1002/mgg3.736. Epub 2019 May 13.

PubMed [citation]

PMID:: 31087512
PMCID:: PMC6625130

New NBIA subtype: genetic, clinical, pathologic, and radiographic features of MPAN.

Hogarth P, Gregory A, Kruer MC, Sanford L, Wagoner W, Natowicz MR, Egel RT, Subramony SH, Goldman JG, Berry-Kravis E, Foulds NC, Hammans SR, Desguerre I, Rodriguez D, Wilson C, Diedrich A, Green S, Tran H, Reese L, Woltjer RL, Hayflick SJ.

Neurology. 2013 Jan 15;80(3):268-75. doi: 10.1212/WNL.0b013e31827e07be. Epub 2012 Dec 26.

PubMed [citation]

PMID:: 23269600
PMCID:: PMC3589182

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV002511576.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

Variant summary: C19orf12 c.83C>T/p.Ser28Phe (legacy name: c.116C>T/p.Ser39Phe) results in a non-conservative amino acid change in the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant was absent in 249450 control chromosomes. The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. c.83C>T has been reported in the literature in individuals affected with Neurodegeneration. These reports do not provide unequivocal conclusions about association of the variant with Neurodegeneration With Brain Iron Accumulation. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as uncertain significance.

#	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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