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NC_000001.11:g.228149860A>G AND Hypomyelinating leukodystrophy 2

Germline classification:
Likely pathogenic (3 submissions)
Last evaluated:
Jun 30, 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:
RCV000023738.16

Allele description [Variation Report for NC_000001.11:g.228149860A>G]

NC_000001.11:g.228149860A>G

Gene:
GJC2:gap junction protein gamma 2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
1q42.13
Genomic location:
Preferred name:
NC_000001.11:g.228149860A>G
Other names:
167G>A; -7899A>G
HGVS:
  • NC_000001.11:g.228149860A>G
  • NG_011838.1:g.5009A>G
  • NM_020435.3:c.-167A>G
  • NC_000001.10:g.228337561A>G
Note:
NCBI staff reviewed the sequence information reported in PubMed 20695017 Fig. 2C to determine the location of this variant on the current reference sequence.
Nucleotide change:
-167A-G
Links:
OMIM: 608803.0011; dbSNP: rs587776888
NCBI 1000 Genomes Browser:
rs587776888
Observations:
8

Condition(s)

Name:
Hypomyelinating leukodystrophy 2
Synonyms:
PELIZAEUS-MERZBACHER-LIKE DISEASE, 1
Identifiers:
MONDO: MONDO:0012125; MedGen: C1837355; Orphanet: 280270; Orphanet: 280282; OMIM: 608804

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000045029OMIM
no assertion criteria provided
Pathogenic
(Jan 1, 2012)
germlineliterature only

PubMed (5)
[See all records that cite these PMIDs]

SCV000882693GeneReviews
no classification provided
not providedgermlineliterature only

PubMed (4)
[See all records that cite these PMIDs]

SCV005199909Molecular Diagnostics Lab, Nemours Children's Health, Delaware
criteria provided, single submitter

(ACMG Guidelines, 2015)
likely pathogenic
(Jun 30, 2021)
unknownclinical testing

PubMed (5)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedliterature only
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only
not providedunknownyes4not providednot provided4not providedclinical testing
not providedunknownno4not providednot provided4not providedclinical testing

Citations

PubMed

Pelizaeus-Merzbacher-like disease: female case report.

Nezu A, Kimura S, Uehara S, Osaka H, Kobayashi T, Haraguchi M, Inoue K, Kawanishi C.

Brain Dev. 1996 Mar-Apr;18(2):114-8.

PubMed [citation]
PMID:
8733901

Relevance of GJC2 promoter mutation in Pelizaeus-Merzbacher-like disease.

Combes P, Kammoun N, Monnier A, Gonthier-Guéret C, Giraud G, Bertini E, Chahnez T, Fakhfakh F, Boespflug-Tanguy O, Vaurs-Barrière C.

Ann Neurol. 2012 Jan;71(1):146-8. doi: 10.1002/ana.22295. Epub 2011 Jan 18. No abstract available.

PubMed [citation]
PMID:
21246605
See all PubMed Citations (10)

Details of each submission

From OMIM, SCV000045029.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (5)

Description

In a Japanese female with a mild Pelizaeus-Merzbacher-like disorder (HLD2; 608804) who was previously reported by Nezu et al. (1996), Osaka et al. (2010) identified a homozygous -167A-G mutation within the proximal GJC2 promoter that segregated with the disorder. The patient's healthy, second-cousin parents were heterozygous for the mutation, which was not found in 122 normal Japanese chromosomes. The mutation is located within a critical SOX10 binding site (site D) in the syntenic mouse Gjc2 proximal promoter and diminishes the consensus of the SOX binding sequence. Functional studies on the mouse promoter indicated that the -167A-G mutation abolishes SOX10 binding to the GJC2 promoter, resulting in a dramatic attenuation of GJC2 transcription.

Combes et al. (2012) identified the -167A-G mutation in 7 patients with a disorder similar to that in the Japanese patient reported by Osaka et al. (2010). The mutation was homozygous in 5 patients from 4 unrelated families from the same area of south Tunisia and segregated with the disease in a consanguineous family with 2 affected members; it was also found in 2 unrelated patients from the Mediterranean area in compound heterozygosity with another mutation in the GJC2 gene that had been identified by Henneke et al. (2008) in patients with HLD2. The mutation was not found in 212 healthy individuals from the same geographic regions. Functional studies in COS-7 and HEK293 cells demonstrated a higher luciferase expression with the mutated promoter than with the wildtype, suggesting a possible difference in transcription factor recruitment.

Using a new reporter luciferase assay in a human glioblastoma cell line (U138), Gotoh et al. (2014) demonstrated that the -167A-G mutation reduced transcriptional activity compared to wildtype in response to SOX10 (602229). The findings suggested that the mutation disrupts SOX10 binding, resulting in a decrease in the GJC2 expression that is important for the maintenance of myelinating oligodendrocytes.

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

From GeneReviews, SCV000882693.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (4)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Molecular Diagnostics Lab, Nemours Children's Health, Delaware, SCV005199909.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing
(GTR000263048.3)
PubMed (5)
2not provided1not providednot providedclinical testing
(GTR000263048.3)
PubMed (5)
3not provided1not providednot providedclinical testing
(GTR000263048.3)
PubMed (5)
4not provided1not providednot providedclinical testing
(GTR000263048.3)
PubMed (5)
5not provided1not providednot providedclinical testing
(GTR000263048.3)
PubMed (5)
6not provided1not providednot providedclinical testing
(GTR000263048.3)
PubMed (5)
7not provided1not providednot providedclinical testing
(GTR000263048.3)
PubMed (5)
8not provided1not providednot providedclinical testing
(GTR000263048.3)
PubMed (5)

Description

This variant (c.-167A>G, promoter region) has not been observed in population databases (gnomAD). The change has been reported in the literature (it has been shown to segregate with the condition), and functional studies indicate a decrease in protein expression (PMID 24374284, PMID 21246605, PMID 20695017, PMID 21959080, PMID 23242375). It was found as homozygous in affected individuals in two unrelated families, and heterozygous in another affected individual also heterozygous for c.893_942del (p.Val298Alafs*33, likely pathogenic), although no parental studies were performed.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyes1bloodnot provided
(GTR000263048.3)
1not providednot providednot provided
2unknownyes1bloodnot provided
(GTR000263048.3)
1not providednot providednot provided
3unknownyes1bloodnot provided
(GTR000263048.3)
1not providednot providednot provided
4unknownyes1bloodnot provided
(GTR000263048.3)
1not providednot providednot provided
5unknownno1bloodnot provided
(GTR000263048.3)
1not providednot providednot provided
6unknownno1bloodnot provided
(GTR000263048.3)
1not providednot providednot provided
7unknownno1bloodnot provided
(GTR000263048.3)
1not providednot providednot provided
8unknownno1bloodnot provided
(GTR000263048.3)
1not providednot providednot provided

Last Updated: Nov 24, 2024