AtlasGene
KRIT1
KRIT1 ankyrin repeat containing
- HGNC 1573↗(opens in a new tab)
- Ensembl gene ENSG00000001631↗(opens in a new tab)
- NCBI Gene 889↗(opens in a new tab)
Summary
- Cytogenetic location
- 7q21.2
- Coordinates
- Chromosome 7: 92,199,413–92,245,914 (GRCh38)
- Exons
- 19 exons across 46.5 kb
- Protein
- 736 amino acids
- Also known as
- CAM
- Previous symbols
- CCM1
- MANE Select transcript
- ENST00000394505.7NM_194454.3
- Locus type
- Protein-coding
- Very high
- Confident
- Low
- Very low
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Get my Genome TestCurated report relevant to this gene
Cerebral Cavernous Malformation
- Cerebral Cavernous Malformation 1Autosomal dominant
- 5 GenCC submitters rate it definitive or strong
How KRIT1 is laid out
- Coding sequence
- Untranslated region
- Intron
- Direction of transcription
- Known disease-causing sites
- Stretches short reads find hard
Exons of the gene's MANE Select transcript (release v1.5), from NCBI and EMBL-EBI, on the GRCh38 reference genome.
Chromosome bands from UCSC's GRCh38 ideogram (2022-10-29).
Nearby genes from Ensembl release 116, on GRCh38.
Exons make up 4.1 kb of the gene's 46.5 kb; 2,211 of those bases code for the protein.
Sequencing KRIT1
2Easy
How hard KRIT1 is to sequence with short reads, out of 100
0 · Easy100 · Hard
Almost all of KRIT1's exons sit where short reads map cleanly.
What adds to it: the share of KRIT1's exons in each kind of hard region
- MappabilityStretches where 100 or 250 bp reads cannot be placed uniquely, so a call there may be missing or wrong. Weight 35%.0%
- HomologySegmental duplications: copies elsewhere in the genome, such as paralogues and pseudogenes, at 90% identity or more. Weight 30%.0%
- RepeatsTandem repeats and runs of one base, which reads slip on and may not span. Weight 15%.2.7%
- GC contentWindows under 25% or over 65% G and C, which library preparation covers thinly. Weight 10%.16%
- Reference coverageGaps in the reference assembly nearby, where there is no sequence for reads to align to. Weight 10%.0%
A Dante Labs score from our own research, built on NIST's Genome in a Bottle maps of hard-to-sequence regions.How it's scoredEach bar is the share of KRIT1's exon bases in that kind of difficult region. The score weighs them by how much each costs a short-read call: 0 when no base is in any, 100 when every base is in all of them.
250
positions in KRIT1 where ClinVar classes a change as pathogenic or likely pathogenic
None of them falls in a region short reads find hard.
A whole genome covers all 46.5 kb of KRIT1, introns included, not only the 4.1 kb of exons.
ClinVar pathogenic variants (275)
The KRIT1 variants ClinVar classifies pathogenic or likely pathogenic for any condition, reviewed by at least one submitter with criteria, and the most reviewed of them. It is ClinVar's public record of the gene, never a result.
- Pathogenic 248
- Pathogenic/likely pathogenic 3
- Likely pathogenic 24
| Variant | Conditions | ClinVar classification | Review status |
|---|---|---|---|
| NM_194454.3(KRIT1):c.2119_2120del (p.Ser707fs) (opens in a new tab) | cerebral cavernous malformation | Pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_194454.3(KRIT1):c.2025+1G>A (opens in a new tab) | cerebral cavernous malformation | Pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_194454.3(KRIT1):c.1905T>A (p.Tyr635Ter) (opens in a new tab) | cerebral cavernous malformation | Pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_194454.3(KRIT1):c.1730+4_1730+7del (opens in a new tab) | cerebral cavernous malformation | Pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_194454.3(KRIT1):c.1389_1390del (p.Ile463fs) (opens in a new tab) | cerebral cavernous malformation | Pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_194454.3(KRIT1):c.1372C>T (p.Gln458Ter) (opens in a new tab) | cerebral cavernous malformation | Pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_194454.3(KRIT1):c.1363C>T (p.Gln455Ter) (opens in a new tab) | cerebral cavernous malformation | Pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_194454.3(KRIT1):c.1267C>T (p.Arg423Ter) (opens in a new tab) | cerebral cavernous malformation | Pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_194454.3(KRIT1):c.1255-1_1256del (opens in a new tab) | cerebral cavernous malformation | Pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_194454.3(KRIT1):c.1255-2A>G (opens in a new tab) | cerebral cavernous malformation | Pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_194454.3(KRIT1):c.902C>G (p.Ser301Ter) (opens in a new tab) | cavernous hemangioma and 1 other | Pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_194454.3(KRIT1):c.880C>T (p.Arg294Ter) (opens in a new tab) | cerebral cavernous malformation | Pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_194454.3(KRIT1):c.729+1G>A (opens in a new tab) | cerebral cavernous malformation | Pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_194454.3(KRIT1):c.535C>T (p.Arg179Ter) (opens in a new tab) | cerebral cavernous malformation | Pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_194454.3(KRIT1):c.397dup (p.Tyr133fs) (opens in a new tab) | cerebral cavernous malformation | Pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_194454.3(KRIT1):c.268C>T (p.Arg90Ter) (opens in a new tab) | cerebral cavernous malformation and 1 other | Pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_194454.3(KRIT1):c.196C>T (p.Gln66Ter) (opens in a new tab) | cerebral cavernous malformation | Pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_194454.3(KRIT1):c.152_155del (p.Lys51fs) (opens in a new tab) | cerebral cavernous malformation and 1 other | Pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_194454.3(KRIT1):c.1927C>T (p.Gln643Ter) (opens in a new tab) | cerebral cavernous malformation | Pathogenic/likely pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_194454.3(KRIT1):c.1730+3A>C (opens in a new tab) | cerebral cavernous malformation | Pathogenic/likely pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_194454.3(KRIT1):c.146_147del (p.Arg49fs) (opens in a new tab) | cerebral cavernous malformation | Pathogenic/likely pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_194454.3(KRIT1):c.410A>G (p.Asp137Gly) (opens in a new tab) | cerebral cavernous malformation | Likely pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_194454.3(KRIT1):c.2143-1G>A (opens in a new tab) | cerebral cavernous malformation | Pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
| NM_194454.3(KRIT1):c.2143-2A>T (opens in a new tab) | cerebral cavernous malformation | Pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
| NM_194454.3(KRIT1):c.2084_2142+81del (opens in a new tab) | cerebral cavernous malformation | Pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
See all 275 with every other KRIT1 variant in ClinVar → (opens in a new tab)
Traits linked to KRIT1
The Human Phenotype Ontology lists these as features of the rare conditions KRIT1 can cause. Each trait's page lists the other genes linked to it.
Abnormality of the cardiovascular system
- Cerebral cavernous malformation
- Collection of dilated blood vessels that forms mass
- Strawberry mark
- Choroidal hemangioma
- Retinal cavernous hemangioma
- Vascular skin abnormality
- Venous malformation
- Developmental retinal vascular malformation
Show 1 more trait
External links
Gene records
Transcript
Protein
Where this comes from
- HGNC: the gene's symbol, name, other symbols and location.
- MANE Select v1.5, from NCBI and EMBL-EBI: the transcript, its exons and coding sequence.
- GenCC and ClinGen, released 2026-10-18: which conditions the gene is linked to, and how strongly.
- The ACMG secondary findings list, SF v3.2.
- ClinVar and the GIAB stratifications: known disease-causing sites, and the regions short reads find hard.
- The Genome in a Bottle genome stratifications, from NIST: the sequencing difficulty score.
- The Human Phenotype Ontology, release 2026-09-01: the traits linked to the gene. Find out more at hpo.jax.org.
- Data release 2026.10.18-8b139e39.
Cite this page
Dante Labs. (n.d.). KRIT1 gene: KRIT1 ankyrin repeat containing. Retrieved 18 October 2026, from https://dantelabs.com/genes/krit1
Dante Labs. KRIT1 gene: KRIT1 ankyrin repeat containing [Internet]. [cited 18 October 2026]. Available from: https://dantelabs.com/genes/krit1
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