KRI1

KRI1 homolog

Basic information

Region (hg38): 19:10553085-10566031

Links

ENSG00000129347 ∙ NCBI:65095 ∙ ∙ HGNC:25769 ∙ Uniprot:Q8N9T8 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the KRI1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KRI1 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				2		2
missense			46	3		49
nonsense						0
start loss			2			2
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	48	5	0

Variants in KRI1

This is a list of pathogenic ClinVar variants found in the KRI1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
19-10553965-T-G		not specified	Uncertain significance (Jul 22, 2022)
19-10553970-C-T		not specified	Uncertain significance (Jan 03, 2024)
19-10553986-G-A		not specified	Uncertain significance (Nov 10, 2022)
19-10553997-A-G		not specified	Uncertain significance (Dec 26, 2023)
19-10554003-C-T		not specified	Uncertain significance (Apr 09, 2024)
19-10554018-T-G		not specified	Uncertain significance (Aug 30, 2022)
19-10554052-G-A		not specified	Uncertain significance (Nov 05, 2021)
19-10554061-C-T		not specified	Uncertain significance (May 18, 2022)
19-10554075-A-G		not specified	Likely benign (May 26, 2023)
19-10554097-G-A		not specified	Uncertain significance (Jul 14, 2021)
19-10554168-T-C		not specified	Uncertain significance (Oct 12, 2021)
19-10554187-G-A		not specified	Uncertain significance (Oct 26, 2021)
19-10554197-G-C		not specified	Uncertain significance (Jul 20, 2021)
19-10554210-G-T		not specified	Uncertain significance (Feb 15, 2023)
19-10554267-G-A		not specified	Uncertain significance (Apr 13, 2022)
19-10555088-C-G		not specified	Uncertain significance (Sep 26, 2023)
19-10555117-C-T		not specified	Uncertain significance (Feb 06, 2023)
19-10555152-C-T			Likely benign (Mar 01, 2023)
19-10555153-G-A		not specified	Uncertain significance (Dec 21, 2022)
19-10555154-C-A		not specified	Uncertain significance (Feb 23, 2023)
19-10555156-C-T		not specified	Uncertain significance (Jun 10, 2024)
19-10555157-G-A		not specified	Uncertain significance (Nov 09, 2022)
19-10555319-G-A		not specified	Uncertain significance (Sep 16, 2021)
19-10555343-C-T		not specified	Uncertain significance (Feb 06, 2024)
19-10557604-C-T		not specified	Uncertain significance (Oct 18, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KRI1	protein_coding	protein_coding	ENST00000312962	19	12953

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.04e-15	0.936	125663	0	85	125748	0.000338

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.139	430	438	0.981	0.0000288	4645
Missense in Polyphen		106	118.9	0.89154		1274
Synonymous	0.994	162	179	0.905	0.0000123	1237
Loss of Function	2.24	30	46.5	0.646	0.00000226	547

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000722	0.000597
Ashkenazi Jewish	0.00	0.00
East Asian	0.000544	0.000544
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000336	0.000299
Middle Eastern	0.000544	0.000544
South Asian	0.000719	0.000719
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0943

Intolerance Scores

• loftool: 0.955
• rvis_EVS: 1.54
• rvis_percentile_EVS: 95.59

Haploinsufficiency Scores

• pHI: 0.274
• hipred: Y
• hipred_score: 0.646
• ghis: 0.443

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.853

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Kri1

Zebrafish Information Network

• Gene name: kri1
• Affected structure: ventral wall of dorsal aorta
• Phenotype tag: abnormal
• Phenotype quality: normal amount

Gene ontology

• Biological process: endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• Cellular component: nucleolus;90S preribosome
• Molecular function: RNA binding