NC_012920.1(MT-CYB):m.616T>C AND Interstitial nephritis

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jul 7, 2021
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:: RCV001804724.3

Allele description [Variation Report for NC_012920.1(MT-CYB):m.616T>C]

NC_012920.1(MT-CYB):m.616T>C

Gene:

MT-TF:mitochondrially encoded tRNA phenylalanine [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Genomic location:

Preferred name:

NC_012920.1(MT-CYB):m.616T>C

HGVS:

NC_012920.1:m.616T>C
NC_012920.1:g.616T>C

Nucleotide change:

616T-C

Links:

OMIM: 590070.0004; dbSNP: rs387906420

NCBI 1000 Genomes Browser:

rs387906420

Condition(s)

Name:: Interstitial nephritis
Synonyms:: Tubulointerstitial nephritis
Identifiers:: MONDO: MONDO:0001085; MedGen: C0041349; Human Phenotype Ontology: HP:0001970

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001745859	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	criteria provided, single submitter (mtDNA variant interpretation)	Pathogenic (Jul 7, 2021)	maternal	clinical testing

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001745859

Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+

criteria provided, single submitter

(mtDNA variant interpretation)

Pathogenic
(Jul 7, 2021)

maternal

clinical testing

Help

Summary from all submissions

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

Details of each submission

From Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+, SCV001745859.1

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

Description

Individual 13.III.2 in the paper by Viering et al. (2021)

Individual 13.II.2 in the paper by Viering et al.(2021)

Individual 13.II.7 in the paper by Viering et al.(2021)

Index (individual 13.III.3) in the paper by Viering et al.(2021)

Description

The m.616T>C variant was observed in 1 family affected by tubulo-interstitial kidney disease (Connor et al. 2017). At least two members of this family were later found to additionally suffer from hypomagnesemia and hypokalemia.(Viering et al. 2021) The homoplasmic variant cosegregated with disease. The variant was scored as pathogenic based on the system published by Wong et al. (2020): PS5, PM7, PM9, PM10.

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

Last Updated: Feb 16, 2025

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