NM_025099.6(CTC1):c.724_727del (p.Lys242fs) AND Cerebroretinal microangiopathy with calcifications and cysts 1
- Germline classification:
- Pathogenic (10 submissions)
- Last evaluated:
- Apr 6, 2025
- Review status:
- 2 stars out of maximum of 4 starscriteria provided, multiple submitters, no conflicts
- Somatic classification
of clinical impact: - None
- Review status:
- (0/4) 0 stars out of maximum of 4 starsno assertion criteria provided
- Somatic classification
of oncogenicity: - None
- Review status:
- (0/4) 0 stars out of maximum of 4 starsno assertion criteria provided
- Record status:
- current
- Accession:
- RCV000023986.28
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
This HGVS expression did not pass validation- Protein change:
- K242fs
- Links:
- OMIM: 613129.0001; dbSNP: rs199473674
- Molecular consequence:
- NM_025099.6:c.724_727del - frameshift variant - [Sequence Ontology: SO:0001589]
Condition(s)
Assertion and evidence details
| Submission Accession | Submitter | Review Status (Assertion method) | Clinical Significance (Last evaluated) | Origin | Method | Citations |
|---|---|---|---|---|---|---|
| SCV000045277 | OMIM | no assertion criteria provided | Pathogenic (Aug 1, 2012) | germline | literature only | |
| SCV000914805 | Illumina Laboratory Services, Illumina | criteria provided, single submitter (ICSL Variant Classification Criteria 09 May 2019) | Pathogenic (Oct 19, 2018) | germline | clinical testing | |
| SCV002019764 | Revvity Omics, Revvity | criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic (Dec 18, 2023) | germline | clinical testing | |
| SCV002055623 | Genome-Nilou Lab | criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic (Jul 15, 2021) | germline | clinical testing | |
| SCV002785788 | Fulgent Genetics, Fulgent Genetics | criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic (Apr 29, 2024) | germline | clinical testing | |
| SCV004183556 | Baylor Genetics | criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic (Oct 24, 2023) | unknown | clinical testing | |
| SCV004803847 | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015) | Pathogenic (Jan 18, 2024) | germline | clinical testing | |
| SCV005878624 | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | criteria provided, single submitter (ARUP Molecular Germline Variant Investigation Process 2024) | Pathogenic (Feb 6, 2025) | germline | clinical testing | |
| SCV006084753 | Victorian Clinical Genetics Services, Murdoch Childrens Research Institute | criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic (Nov 26, 2024) | germline | clinical testing | |
| SCV006584525 | 3billion | criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic (Apr 6, 2025) | germline | clinical testing |
Summary from all submissions
| Ethnicity | Origin | Affected | Individuals | Families | Chromosomes tested | Number Tested | Family history | Method |
|---|---|---|---|---|---|---|---|---|
| not provided | germline | not provided | not provided | not provided | not provided | not provided | not provided | literature only |
| not provided | unknown | unknown | not provided | not provided | not provided | not provided | not provided | clinical testing |
| not provided | germline | no | not provided | not provided | not provided | not provided | not provided | clinical testing |
| not provided | germline | yes | not provided | not provided | not provided | not provided | not provided | clinical testing |
| not provided | germline | unknown | not provided | not provided | not provided | not provided | not provided | clinical 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.
- 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.
- PMID:
- 22899577
- PMCID:
- PMC3659926
Details of each submission
From OMIM, SCV000045277.4
| # | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
|---|---|---|---|---|---|---|
| 1 | not provided | not provided | not provided | not provided | literature 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.
| # | 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 | not provided | not provided | not provided | |
From Illumina Laboratory Services, Illumina, SCV000914805.1
| # | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
|---|---|---|---|---|---|---|
| 1 | not provided | not provided | not provided | not provided | clinical 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.
| # | Sample | Method | Observation | |||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
| 1 | germline | unknown | not provided | not provided | not provided | not provided | not provided | not provided | not provided | |
From Revvity Omics, Revvity, SCV002019764.4
| # | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
|---|---|---|---|---|---|---|
| 1 | not provided | not provided | not provided | not provided | clinical testing | PubMed (1) |
| # | Sample | Method | Observation | |||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
| 1 | germline | unknown | not provided | not provided | not provided | not provided | not provided | not provided | not provided | |
From Genome-Nilou Lab, SCV002055623.1
| # | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
|---|---|---|---|---|---|---|
| 1 | not provided | not provided | not provided | not provided | clinical testing | PubMed (1) |
| # | Sample | Method | Observation | |||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
| 1 | germline | no | not provided | not provided | not provided | not provided | not provided | not provided | not provided | |
From Fulgent Genetics, Fulgent Genetics, SCV002785788.2
| # | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
|---|---|---|---|---|---|---|
| 1 | not provided | not provided | not provided | not provided | clinical testing | PubMed (1) |
| # | Sample | Method | Observation | |||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
| 1 | germline | unknown | not provided | not provided | not provided | not provided | not provided | not provided | not provided | |
From Baylor Genetics, SCV004183556.1
| # | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
|---|---|---|---|---|---|---|
| 1 | not provided | not provided | not provided | not provided | clinical testing | PubMed (1) |
| # | Sample | Method | Observation | |||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
| 1 | unknown | unknown | not provided | not provided | not provided | not provided | not provided | not provided | not provided | |
From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV004803847.1
| # | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
|---|---|---|---|---|---|---|
| 1 | not provided | not provided | not provided | not provided | clinical 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.
| # | Sample | Method | Observation | |||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
| 1 | germline | unknown | not provided | not provided | not provided | not provided | not provided | not provided | not provided | |
From ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories, SCV005878624.2
| # | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
|---|---|---|---|---|---|---|
| 1 | not provided | not provided | not provided | not provided | clinical testing | not 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
| # | Sample | Method | Observation | |||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
| 1 | germline | unknown | not provided | not provided | not provided | not provided | not provided | not provided | not provided | |
From Victorian Clinical Genetics Services, Murdoch Childrens Research Institute, SCV006084753.3
| # | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
|---|---|---|---|---|---|---|
| 1 | not provided | not provided | not provided | not provided | clinical testing | PubMed (1) |
Description
This variant is classified as Pathogenic. Evidence in support of pathogenic classification: Variant is predicted to cause nonsense-mediated decay (NMD) and loss of protein (premature termination codon is located at least 54 nucleotides upstream of the final exon-exon junction); Variant is present in gnomAD <0.01 for a recessive condition (v4: 448 heterozygote(s), 0 homozygote(s)); This variant has strong previous evidence of pathogenicity in unrelated individuals.This variant has been classified as pathogenic twelve times by clinical laboratories in ClinVar; Other NMD-predicted variants comparable to the one identified in this case have very strong previous evidence for pathogenicity. Many NMD-predicted variants have been classified as pathogenic or likely pathogenic by clinical laboratories in ClinVar. Additional information: This variant is heterozygous; This gene is associated with autosomal recessive disease; Loss of function is a known mechanism of disease in this gene and is associated with cerebroretinal microangiopathy with calcifications and cysts (MIM#612199); Inheritance information for this variant is not currently available in this individual.
| # | 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 3billion, SCV006584525.1
| # | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
|---|---|---|---|---|---|---|
| 1 | not provided | not provided | not provided | not provided | clinical testing | PubMed (2) |
Description
The variant is observed at an extremely low frequency in the gnomAD v4.1.0 dataset (total allele frequency: 0.028%). Predicted Consequence/Location: Frameshift: predicted to result in a loss or disruption of normal protein function through nonsense-mediated decay (NMD) or protein truncation. Multiple pathogenic variants are reported downstream of the variant. The variant has been reported at least twice as pathogenic with clinical assertions and evidence for the classification (ClinVar ID: VCV000030995 / PMID: 22267198). Therefore, this variant is classified as Pathogenic according to the recommendation of ACMG/AMP guideline.
| # | 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 | |
Last Updated: Apr 12, 2026