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NM_153689.6(C2orf69):c.298del (p.Gln100fs) AND Combined oxidative phosphorylation deficiency 53

Germline classification:
Pathogenic/Likely pathogenic (3 submissions)
Last evaluated:
Mar 28, 2025
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:
RCV001533283.6

Allele description [Variation Report for NM_153689.6(C2orf69):c.298del (p.Gln100fs)]

NM_153689.6(C2orf69):c.298del (p.Gln100fs)

Gene:
C2orf69:chromosome 2 open reading frame 69 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
2q33.1
Genomic location:
Preferred name:
NM_153689.6(C2orf69):c.298del (p.Gln100fs)
Other names:
C2ORF69, 1-BP DEL, 298C
HGVS:
  • NC_000002.12:g.199911736del
  • NM_153689.6:c.298delMANE SELECT
  • NP_710156.3:p.Gln100fs
  • NC_000002.11:g.200776459del
  • NM_153689.5:c.298del
  • NM_153689.6:c.298delCMANE SELECT
Protein change:
Q100fs
Links:
OMIM: 619219.0001; dbSNP: rs2077262520
NCBI 1000 Genomes Browser:
rs2077262520
Molecular consequence:
  • NM_153689.6:c.298del - frameshift variant - [Sequence Ontology: SO:0001589]
Observations:
1

Condition(s)

Name:
Combined oxidative phosphorylation deficiency 53 (COXPD53)
Synonyms:
GLOBAL DEVELOPMENTAL DELAY, PROGRESSIVE MICROCEPHALY, STRUCTURAL BRAIN ABNORMALITIES, AND AUTOINFLAMMATION; ELBRACHT-ISIKAY SYNDROME
Identifiers:
MONDO: MONDO:0030378; MedGen: C5543631; OMIM: 619423

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001749100OMIM
no assertion criteria provided
Pathogenic
(Jul 9, 2021)
germlineliterature only

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

SCV001983771Institute for Human Genetics and Genomic Medicine, Uniklinik RWTH Aachen
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenicinheritedclinical testing

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

SCV005911400Institute of Human Genetics, University of Leipzig Medical Center
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely pathogenic
(Mar 28, 2025)
inheritedclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only
not providedinheritedyes1not providednot providednot providednot providedclinical testing

Citations

PubMed

C2orf69 mutations disrupt mitochondrial function and cause a multisystem human disorder with recurring autoinflammation.

Lausberg E, Gießelmann S, Dewulf JP, Wiame E, Holz A, Salvarinova R, van Karnebeek CD, Klemm P, Ohl K, Mull M, Braunschweig T, Weis J, Sommer CJ, Demuth S, Haase C, Stollbrink-Peschgens C, Debray FG, Libioulle C, Choukair D, Oommen PT, Borkhardt A, Surowy H, et al.

J Clin Invest. 2021 Jun 15;131(12). doi:pii: 143078. 10.1172/JCI143078.

PubMed [citation]
PMID:
33945503
PMCID:
PMC8203463

Loss of C2orf69 defines a fatal autoinflammatory syndrome in humans and zebrafish that evokes a glycogen-storage-associated mitochondriopathy.

Wong HH, Seet SH, Maier M, Gurel A, Traspas RM, Lee C, Zhang S, Talim B, Loh AYT, Chia CY, Teoh TS, Sng D, Rensvold J, Unal S, Shishkova E, Cepni E, Nathan FM, Sirota FL, Liang C, Yarali N, Simsek-Kiper PO, Mitani T, et al.

Am J Hum Genet. 2021 Jul 1;108(7):1301-1317. doi: 10.1016/j.ajhg.2021.05.003. Epub 2021 May 25. Erratum in: Am J Hum Genet. 2021 Jul 1;108(7):1356. doi: 10.1016/j.ajhg.2021.06.009..

PubMed [citation]
PMID:
34038740
PMCID:
PMC8322802
See all PubMed Citations (3)

Details of each submission

From OMIM, SCV001749100.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (2)

Description

In 6 patients from 4 families, including 2 unrelated Kurdish patients (families 1 and 2), 2 German sibs (family 3), and 2 Turkish sibs (family 4), with combined oxidative phosphorylation deficiency-53 (COXPD53; 619423), Lausberg et al. (2021) identified homozygosity for a 1-bp deletion (c.298delC, NM_153689.6) in the C2ORF69 gene, resulting in a frameshift and premature termination (Gln100SerfsTer18). The mutation, which was identified by whole-exome sequencing and confirmed by Sanger sequencing, segregated with the disorder in the families. In lymphocytes from one patient, C2ORF69 RNA was at comparable levels to controls, but the protein was absent, indicating instability of the truncated protein.

In 5 patients from 3 families with COXPD53, including 2 Kurdish Turkish sibs (family 1), 2 Iranian sibs (family 4), and an Iraqi patient (family 7), all born of consanguineous parents, Wong et al. (2021) identified homozygosity for the c.298delC mutation in the C2ORF69 gene. The mutation, which was identified by whole-exome sequencing and confirmed by Sanger sequencing, segregated with the disorder in the families. The mutation was not present in the gnomAD (v.2.1.1 and v.3.1) or TOPmed databases or in an in-house database consisting of more than 50,000 genomes/exomes. In family 7, the patient had 4 similarly affected deceased sibs and 1 similarly affected living sib who were not tested for the mutation.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot providednot providednot providednot providednot provided

From Institute for Human Genetics and Genomic Medicine, Uniklinik RWTH Aachen, SCV001983771.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
11not providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1inheritedyesnot providednot providednot provided1not providednot providednot provided

From Institute of Human Genetics, University of Leipzig Medical Center, SCV005911400.1

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

Description

Criteria applied: PVS1_STR,PM2,PM3

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1inheritedyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Apr 28, 2025