NM_025152.3(NUBPL):c.815-27T>C AND not provided

Germline classification:: Conflicting interpretations of pathogenicity (3 submissions)
Last evaluated:: Feb 1, 2023
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:: RCV000198391.27

Allele description [Variation Report for NM_025152.3(NUBPL):c.815-27T>C]

NM_025152.3(NUBPL):c.815-27T>C

Gene:

NUBPL:NUBP iron-sulfur cluster assembly factor, mitochondrial [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

14q12

Genomic location:

Preferred name:

NM_025152.3(NUBPL):c.815-27T>C

HGVS:

NC_000014.9:g.31850092T>C
NG_028349.1:g.293708T>C
NM_001201573.2:c.527-27T>C
NM_001201574.2:c.266-27T>C
NM_025152.3:c.815-27T>CMANE SELECT
NC_000014.8:g.32319298T>C
NM_001201573.1:c.527-27T>C
NM_025152.2:c.815-27T>C
c.815-27T-C

Links:

OMIM: 613621.0001; OMIM: 613621.0008; dbSNP: rs118161496

NCBI 1000 Genomes Browser:

rs118161496

Molecular consequence:

NM_001201573.2:c.527-27T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001201574.2:c.266-27T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_025152.3:c.815-27T>C - intron variant - [Sequence Ontology: SO:0001627]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Lpt (plasmid) [Lacticaseibacillus rhamnosus]
Lpt (plasmid) [Lacticaseibacillus rhamnosus]
gi|1124156553|gb|APQ43788.1|

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000251972	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Pathogenic (Aug 14, 2017)	germline	clinical testing	Citation Link,
SCV000493198	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Uncertain significance (Feb 1, 2023)	germline	clinical testing	Citation Link,
SCV000511195	Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain Significance (Jan 9, 2017)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000251972

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Pathogenic
(Aug 14, 2017)

germline

clinical testing

Citation Link,

SCV000493198

CeGaT Center for Human Genetics Tuebingen

criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)

Uncertain significance
(Feb 1, 2023)

germline

clinical testing

Citation Link,

SCV000511195

Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain Significance
(Jan 9, 2017)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	3	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	not provided	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

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 GeneDx, SCV000251972.10

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

Description

Expression studies of the c.815-27 T>C sequence change found that this variant impairs mRNA splicing resulting in a 80% decrease in complex I assembly and function (Tucker et al., 2012; Wydro et al., 2013). Therefore, based on the currently available information, the c.815-27 T>C variant is a strong candidate for a pathogenic variant; however, the possibility that it is a benign variant cannot be excluded.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From CeGaT Center for Human Genetics Tuebingen, SCV000493198.28

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	3	not provided	not provided	clinical testing	not provided

Description

NUBPL: PM3:Strong, PS3:Moderate, PM2:Supporting, PP3, BS2

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		3	not provided	not provided	not provided

From Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics, SCV000511195.1

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

Description

Converted during submission to Uncertain significance.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	not provided	not provided	not provided	not provided		not provided	0.003245	not provided	not provided

Last Updated: May 12, 2024

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