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NM_031448.6(C19orf12):c.161-2del AND Neurodegeneration with brain iron accumulation 4

Germline classification:
Pathogenic/Likely pathogenic (2 submissions)
Last evaluated:
Sep 1, 2022
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV000503280.7

Allele description [Variation Report for NM_031448.6(C19orf12):c.161-2del]

NM_031448.6(C19orf12):c.161-2del

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.161-2del
Other names:
NP_001026896.2:p.G66_G73del
HGVS:
  • NC_000019.10:g.29702979del
  • NG_031970.2:g.17811del
  • NM_001031726.4:c.161-2del
  • NM_001256046.3:c.161-2del
  • NM_001256047.2:c.161-2del
  • NM_001282929.1:c.-32-2del
  • NM_001282930.3:c.-32-2del
  • NM_001282931.3:c.-32-2del
  • NM_031448.6:c.161-2delMANE SELECT
  • NC_000019.9:g.30193886del
  • NM_001031726.2:c.194-2del
  • NM_001031726.3:c.194-2delA
Links:
dbSNP: rs1352744778
NCBI 1000 Genomes Browser:
rs1352744778
Molecular consequence:
  • NM_001031726.4:c.161-2del - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001256046.3:c.161-2del - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001256047.2:c.161-2del - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001282929.1:c.-32-2del - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001282930.3:c.-32-2del - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001282931.3:c.-32-2del - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_031448.6:c.161-2del - splice acceptor variant - [Sequence Ontology: SO:0001574]
Observations:
1

Condition(s)

Name:
Neurodegeneration with brain iron accumulation 4 (NBIA4)
Synonyms:
MITOCHONDRIAL PROTEIN-ASSOCIATED NEURODEGENERATION
Identifiers:
MONDO: MONDO:0013674; MedGen: C3280371; Orphanet: 289560; OMIM: 614298

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000593800Genetic Services Laboratory, University of Chicago
criteria provided, single submitter

(ACMG Guidelines, 2015)		Pathogenic
(Aug 26, 2016) 		germlineclinical testing

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

SCV0025732593billion
criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely pathogenic
(Sep 1, 2022) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not providednot provided1not providedclinical testing

Citations

PubMed

Targeted exome analysis identifies the genetic basis of disease in over 50% of patients with a wide range of ataxia-related phenotypes.

Sun M, Johnson AK, Nelakuditi V, Guidugli L, Fischer D, Arndt K, Ma L, Sandford E, Shakkottai V, Boycott K, Warman-Chardon J, Li Z, Del Gaudio D, Burmeister M, Gomez CM, Waggoner DJ, Das S.

Genet Med. 2019 Jan;21(1):195-206. doi: 10.1038/s41436-018-0007-7. Epub 2018 Jun 18.

PubMed [citation]
PMID:
29915382
PMCID:
PMC6524765

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From Genetic Services Laboratory, University of Chicago, SCV000593800.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From 3billion, SCV002573259.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (2)

Description

The variant is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: <0.001%). Canonical splice site is predicted to alter splicing and result in a loss or disruption of normal protein function. The predicted truncated protein may be shortened by more than 10%. Multiple pathogenic variants are reported downstream of the variant. The variant has been reported to be associated with C19orf12-related disorder (ClinVar ID: VCV000434550 / PMID: 29915382). Therefore, this variant is classified as Likely pathogenic according to the recommendation of ACMG/AMP guideline.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyes1not providednot provided1not providednot providednot provided

Last Updated: Nov 3, 2024