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NM_025099.6(CTC1):c.724_727del (p.Lys242fs) AND Cerebroretinal microangiopathy with calcifications and cysts 1

Germline classification:
Pathogenic (8 submissions)
Last evaluated:
Apr 29, 2024
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:
RCV000023986.22

Allele description [Variation Report for NM_025099.6(CTC1):c.724_727del (p.Lys242fs)]

NM_025099.6(CTC1):c.724_727del (p.Lys242fs)

Gene:
CTC1:CST telomere replication complex component 1 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
17p13.1
Genomic location:
Preferred name:
NM_025099.6(CTC1):c.724_727del (p.Lys242fs)
Other names:
p.Lys242Leufs*41
HGVS:
  • NC_000017.11:g.8237442_8237445del
  • NG_032148.2:g.15653_15656del
  • NM_025099.6:c.724_727delMANE SELECT
  • NP_079375.3:p.Lys242fs
  • LRG_1124t1:c.724_727del
  • LRG_1124:g.15653_15656del
  • LRG_1124p1:p.Lys242fs
  • NC_000017.10:g.8140758_8140761del
  • NC_000017.10:g.8140760_8140763del
  • NM_025099.5:c.724_727delAAAG
  • NM_025099.6:c.724_727delAAAGMANE SELECT
Protein change:
K242fs
Links:
OMIM: 613129.0001; dbSNP: rs199473674
NCBI 1000 Genomes Browser:
rs199473674
Molecular consequence:
  • NM_025099.6:c.724_727del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:
Cerebroretinal microangiopathy with calcifications and cysts 1 (CRMCC1)
Identifiers:
MONDO: MONDO:0024564; MedGen: C4552029; Orphanet: 313838; OMIM: 612199

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000045277OMIM
no assertion criteria provided
Pathogenic
(Aug 1, 2012)
germlineliterature only

PubMed (3)
[See all records that cite these PMIDs]

SCV000914805Illumina Laboratory Services, Illumina
criteria provided, single submitter

(ICSL Variant Classification Criteria 09 May 2019)
Pathogenic
(Oct 19, 2018)
germlineclinical testing

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

Citation Link,

SCV002019764Revvity Omics, Revvity
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Dec 18, 2023)
germlineclinical testing

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

SCV002055623Genome-Nilou Lab
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Jul 15, 2021)
germlineclinical testing

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

SCV002785788Fulgent Genetics, Fulgent Genetics
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Apr 29, 2024)
germlineclinical testing

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

SCV004183556Baylor Genetics
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Oct 24, 2023)
unknownclinical testing

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

SCV004803847Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)
Pathogenic
(Jan 18, 2024)
germlineclinical testing

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

Citation Link,

SCV005878624ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
criteria provided, single submitter

(ARUP Molecular Germline Variant Investigation Process 2024)
Pathogenic
(Jan 5, 2024)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing
not providedgermlinenonot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Cerebroretinal microangiopathy with calcifications and cysts (CRMCC).

Briggs TA, Abdel-Salam GM, Balicki M, Baxter P, Bertini E, Bishop N, Browne BH, Chitayat D, Chong WK, Eid MM, Halliday W, Hughes I, Klusmann-Koy A, Kurian M, Nischal KK, Rice GI, Stephenson JB, Surtees R, Talbot JF, Tehrani NN, Tolmie JL, Toomes C, et al.

Am J Med Genet A. 2008 Jan 15;146A(2):182-90.

PubMed [citation]
PMID:
18076099

Mutations in the telomere capping complex in bone marrow failure and related syndromes.

Walne AJ, Bhagat T, Kirwan M, Gitiaux C, Desguerre I, Leonard N, Nogales E, Vulliamy T, Dokal IS.

Haematologica. 2013 Mar;98(3):334-8. doi: 10.3324/haematol.2012.071068. Epub 2012 Aug 16.

PubMed [citation]
PMID:
22899577
PMCID:
PMC3659926
See all PubMed Citations (7)

Details of each submission

From OMIM, SCV000045277.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (3)

Description

In 2 Scottish sisters and an unrelated English patient, all with Coats plus syndrome (CRMCC1; 612199), Anderson et al. (2012) identified compound heterozygosity for 2 mutations in the CTC1 gene: a 4-bp deletion (724_727delAAAG) in exon 5, resulting in a frameshift and premature termination, and a 2959C-T transition in exon 18, resulting in an arg987-to-trp (R987W; 613129.0002) substitution. The missense mutation affected a residue well-conserved among mammals, and neither mutation was found in 1,730 controls. The patients had previously been reported by Briggs et al. (2008). All had intrauterine growth retardation, intracranial calcifications, leukoencephalopathy, early-onset retinal changes, and gastrointestinal ectasia. The sisters both had gray hair, translucent skin, and dystrophic nails, and the English patient had anemia. One of the sisters and the English patient had early-onset bone fractures. The 2 sisters died in their early twenties of gastrointestinal bleeding. One of the patients was found to have shortened telomere lengths in white blood cells, and each heterozygous parent had telomere lengths at the lower range of normal.

Keller et al. (2012) reported an 18-year-old girl who was compound heterozygous for 724_727delAAAG and a 3-bp deletion (c.2954_2956delGTT; 613129.0012) in the CTC1 gene. The patient presented at age 15 years with classic features of dyskeratosis congenita (see, e.g., 127550), including bone marrow failure, abnormalities in skin pigmentation, nail dysplasia, and graying hair. She also had short stature, osteopenia, decreased pulmonary function, and blurry vision associated with sheathed vessels and microaneurysm formation in the retina. Brain MRI showed calcifications in the right thalamus, and telomeres were shortened significantly. Neurologic function was normal. Patient fibroblasts showed a defect in outgrowth as well as rapid senescence compared to controls. Keller et al. (2012) noted that both CTC1 mutations had been reported in patients with Coats plus syndrome, suggesting that Coats plus syndrome and DKC show phenotypic and genetic overlap, consistent with a telomere-related disease.

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

From Illumina Laboratory Services, Illumina, SCV000914805.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (5)

Description

The CTC1 c.724_727delAAAG (p.Lys242LeufsTer41) variant has been reported in four studies and is found in a total of eight probands in a compound heterozygous state, including two probands with dyskeratosis congenita, five probands with Coats plus syndrome, and one proband with cerebroretinal microangiopathy with calcifications and cysts (Anderson et al. 2012; Keller et al. 2012; Polvi et al. 2012; Walne et al. 2013). Expression of the p.Lys242LeufsTer41 variant protein in mouse embryonic fibroblasts with the wild type copy of CTC1 knocked out, demonstrated increased telomere dysfunction and the formation of fused chromosomes (Gu et al. 2013). Control data are unavailable for this variant, which is reported at a frequency of 0.000523 in the Latino population of the Genome Aggregation Database. Based on the available evidence and the potential impact of frameshift variants, the p.Lys242LeufsTer41 variant is classified as pathogenic for CTC1-related disorders. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population.

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

From Revvity Omics, Revvity, SCV002019764.3

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

From Genome-Nilou Lab, SCV002055623.1

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

From Fulgent Genetics, Fulgent Genetics, SCV002785788.2

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

From Baylor Genetics, SCV004183556.1

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

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV004803847.1

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

Description

Variant summary: CTC1 c.724_727delAAAG (p.Lys242LeufsX41) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. The variant allele was found at a frequency of 0.0002 in 249584 control chromosomes. This frequency is not significantly higher than estimated for a pathogenic variant in CTC1 causing Cerebroretinal Microangiopathy With Calcifications And Cysts 1 (0.0002 vs 0.0011), allowing no conclusion about variant significance. c.724_727delAAAG has been reported in the literature in individuals affected with Cerebroretinal Microangiopathy With Calcifications And Cysts 1 (Anderson_2012). These data indicate that the variant is likely to be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publication have been ascertained in the context of this evaluation (PMID: 22267198). ClinVar contains an entry for this variant (Variation ID: 30995). Based on the evidence outlined above, the variant was classified as pathogenic.

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

From ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories, SCV005878624.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The CTC1 c.724_727del; p.Lys242LeufsTer41variant (rs199473674) is reported in the literature in individuals affected with bone marrow failure syndromes who also carry a pathogenic variant in trans (Keller 2012, Polvi 2012, Shen 2019, Walne 2013). This variant is also reported in ClinVar (Variation ID: 30995). This variant is found in the general population with an overall allele frequency of 0.02% (54/280,872 alleles) in the Genome Aggregation Database (v2.1.1). This variant causes a frameshift by deleting four nucleotides, so it is predicted to result in a truncated protein or mRNA subject to nonsense-mediated decay. Based on available information, this variant is considered to be pathogenic. References: Keller RB et al. CTC1 Mutations in a patient with dyskeratosis congenita. Pediatric blood & cancer. 2012 Aug. PMID: 22532422. Polvi A et al. Mutations in CTC1, encoding the CTS telomere maintenance complex component 1, cause cerebroretinal microangiopathy with calcifications and cysts. Am J Hum Genet. 2012 Mar 9. PMID: 22387016. Shen W et al. Impact of germline CTC1 alterations on telomere length in acquired bone marrow failure. Br J Haematol. 2019 Jun. PMID: 30891747. Walne AJ et al. Mutations in the telomere capping complex in bone marrow failure and related syndromes. Haematologica. 2013 Mar. PMID: 22899577.

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

Last Updated: Mar 11, 2025