NM_031448.6(C19orf12):c.171_181del (p.Gly58fs) AND C19orf12-related disorder

Germline classification:: Pathogenic (1 submission)
Last evaluated:: May 23, 2024
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

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:: RCV003904862.2

Allele description [Variation Report for NM_031448.6(C19orf12):c.171_181del (p.Gly58fs)]

NM_031448.6(C19orf12):c.171_181del (p.Gly58fs)

Gene:

C19orf12:chromosome 19 open reading frame 12 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

19q12

Genomic location:

Preferred name:

NM_031448.6(C19orf12):c.171_181del (p.Gly58fs)

Other names:

C19ORF12, 11-BP DEL, NT204

HGVS:

NC_000019.10:g.29702967_29702977del
NG_031970.2:g.17823_17833del
NM_001031726.4:c.171_181del
NM_001256046.3:c.171_181del
NM_001256047.2:c.171_181del
NM_001282929.1:c.-22_-12del
NM_001282930.3:c.-22_-12del
NM_001282931.3:c.-22_-12del
NM_031448.6:c.171_181delMANE SELECT
NP_001026896.2:p.Gly69fs
NP_001026896.3:p.Gly58fs
NP_001242975.1:p.Gly58fs
NP_001242976.1:p.Gly58fs
NP_113636.2:p.Gly58fs
NC_000019.10:g.29702957_29702967del
NC_000019.9:g.30193864_30193874del
NC_000019.9:g.30193874_30193884del
NM_001031726.2:c.204_214del
NM_001031726.3:c.204_214del
NM_001031726.3:c.204_214del11
NM_001031726.4:c.171_181del11
NP_001026896.2:p.Gly69ArgfsTer10

Protein change:

G58fs

Links:

OMIM: 614297.0001; dbSNP: rs515726204

NCBI 1000 Genomes Browser:

rs515726204

Molecular consequence:

NM_001282929.1:c.-22_-12del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001282930.3:c.-22_-12del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001282931.3:c.-22_-12del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001031726.4:c.171_181del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001256046.3:c.171_181del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001256047.2:c.171_181del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_031448.6:c.171_181del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:: C19orf12-related disorder
Synonyms:: C19orf12-related condition
Identifiers:

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004735215	PreventionGenetics, part of Exact Sciences	no assertion criteria provided	Pathogenic (May 23, 2024)	germline	clinical testing

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004735215

PreventionGenetics, part of Exact Sciences

no assertion criteria provided

Pathogenic
(May 23, 2024)

germline

clinical testing

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

Details of each submission

From PreventionGenetics, part of Exact Sciences, SCV004735215.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

The C19orf12 c.204_214del11 variant is predicted to result in a frameshift and premature protein termination (p.Gly69Argfs*10). This variant has primarily been reported in the homozygous or compound heterozygous states in individuals with autosomal recessive neurodegeneration with brain iron accumulation (see for example, Table 1, Hartig et al. 2011. PubMed ID: 21981780; Table 1, Schulte et al. 2012. PubMed ID: 23436634; Goldman et al. 2013. PubMed ID: 23494994). In these studies heterozygous carriers were reported as unaffected. However, in a single case it has also been associated with autosomal dominant neurodegeneration with brain iron accumulation (Table 1, Sparber et al. 2021. PubMed ID: 33607528). This variant has been classified as pathogenic in the ClinVar database (https://www.ncbi.nlm.nih.gov/clinvar/variation/31155/). Given the evidence, we interpret this variant as pathogenic in the context of autosomal recessive disease, and as a variant of uncertain significance in the context of autosomal dominant disease.

#	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: Oct 8, 2024

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