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NM_194454.3(KRIT1):c.1201_1204del (p.Gln401fs)

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Interpretation:
Conflicting interpretations of pathogenicity​

Pathogenic(3);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
4 (Most recent: Jan 7, 2021)
Last evaluated:
Sep 28, 2019
Accession:
VCV000372398.7
Variation ID:
372398
Description:
4bp microsatellite
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NM_194454.3(KRIT1):c.1201_1204del (p.Gln401fs)

Allele ID
359673
Variant type
Microsatellite
Variant length
4 bp
Cytogenetic location
7q21.2
Genomic location
7: 92225770-92225773 (GRCh38) GRCh38 UCSC
7: 91855084-91855087 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000007.13:g.91855087GTTT[1]
NC_000007.14:g.92225773GTTT[1]
NM_194454.3:c.1201_1204del MANE Select NP_919436.1:p.Gln401fs frameshift
... more HGVS
Protein change
Q353fs, Q401fs, Q163fs
Other names
-
Canonical SPDI
NC_000007.14:92225769:TTTGTTTGTTT:TTTGTTT
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
ClinGen: CA16042598
dbSNP: rs1057517753
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic 2 criteria provided, multiple submitters, no conflicts Nov 21, 2016 RCV000414484.1
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Sep 28, 2019 RCV000816950.4
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
KRIT1 - - GRCh38
GRCh37
353 383

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Pathogenic
(Jun 14, 2016)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
PreventionGenetics,PreventionGenetics
Accession: SCV000852966.1
Submitted: (Oct 12, 2018)
Evidence details
Pathogenic
(Nov 21, 2016)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000490587.2
Submitted: (Jan 29, 2019)
Evidence details
Comment:
The c.1201_1204delCAAA pathogenic variant in the KRIT1 gene has been previously reported in patients with CCM (Rajakulendran et al., 2011; Zhao et al., 2011). The … (more)
Uncertain significance
(Jan 01, 2016)
criteria provided, single submitter
Method: clinical testing
Cerebral cavernous malformation
Allele origin: unknown
Centre for Mendelian Genomics,University Medical Centre Ljubljana
Accession: SCV001366349.2
Submitted: (Nov 24, 2020)
Evidence details
Comment:
This variant was classified as: Uncertain significance. The following ACMG criteria were applied in classifying this variant: PM2,PP4,PP5.
Pathogenic
(Sep 28, 2019)
criteria provided, single submitter
Method: clinical testing
Cerebral cavernous malformation
Allele origin: germline
Invitae
Accession: SCV000957480.3
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (8)
Comment:
This sequence change creates a premature translational stop signal (p.Gln401Thrfs*10) in the KRIT1 gene. It is expected to result in an absent or disrupted protein … (more)

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
Identification of a Novel Deletion Mutation (c.1780delG) and a Novel Splice-Site Mutation (c.1412-1G>A) in the CCM1/KRIT1 Gene Associated with Familial Cerebral Cavernous Malformation in the Chinese Population. Yang C Journal of molecular neuroscience : MN 2017 PMID: 27649701
Familial cerebral cavernomas due to a KRIT1 mutation presenting with epilepsy. Rajakulendran S BMJ case reports 2011 PMID: 22699465
A novel CCM1 gene mutation causes cerebral cavernous malformation in a Chinese family. Zhao Y Journal of clinical neuroscience : official journal of the Neurosurgical Society of Australasia 2011 PMID: 20884211
Novel CCM1, CCM2, and CCM3 mutations in patients with cerebral cavernous malformations: in-frame deletion in CCM2 prevents formation of a CCM1/CCM2/CCM3 protein complex. Stahl S Human mutation 2008 PMID: 18300272
Spectrum and expression analysis of KRIT1 mutations in 121 consecutive and unrelated patients with Cerebral Cavernous Malformations. Cavé-Riant F European journal of human genetics : EJHG 2002 PMID: 12404106
CCM1 gene mutations in families segregating cerebral cavernous malformations. Davenport WJ Neurology 2001 PMID: 11222804
Truncating mutations in CCM1, encoding KRIT1, cause hereditary cavernous angiomas. Laberge-le Couteulx S Nature genetics 1999 PMID: 10508515
Contraceptive use for planned parenthood patients. Savel LE New Jersey medicine : the journal of the Medical Society of New Jersey 1990 PMID: 2359550

Text-mined citations for rs1057517753...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Jun 23, 2021