KRR1

KRR1 small subunit processome component homolog, the group of SSU processome

Basic information

Region (hg38): 12:75490862-75511636

Previous symbols: [ "HRB2" ]

Links

ENSG00000111615 ∙ NCBI:11103 ∙ OMIM:612817 ∙ HGNC:5176 ∙ Uniprot:Q13601 ∙ 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 KRR1 gene.

• Inborn genetic diseases (20 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KRR1 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						0
missense			13	1		14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding			6		1	7
Total	0	0	19	1	1

Variants in KRR1

This is a list of pathogenic ClinVar variants found in the KRR1 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-75495572-T-C			Benign (Jan 30, 2018)
12-75495590-A-G		not specified	Uncertain significance (Jan 26, 2022)
12-75495600-A-G		not specified	Uncertain significance (Sep 13, 2023)
12-75495643-G-C		not specified	Uncertain significance (Sep 27, 2022)
12-75498866-G-C		not specified	Uncertain significance (Dec 06, 2022)
12-75498893-T-C		not specified	Uncertain significance (Sep 14, 2022)
12-75498925-A-G		not specified	Uncertain significance (Jun 02, 2023)
12-75499882-A-G		not specified	Uncertain significance (Mar 23, 2023)
12-75501794-C-A		not specified	Uncertain significance (Jan 10, 2023)
12-75501815-G-T		not specified	Uncertain significance (Jan 11, 2023)
12-75501928-T-C		not specified	Uncertain significance (Nov 19, 2022)
12-75501930-G-A		not specified	Uncertain significance (Aug 02, 2022)
12-75501945-C-T		not specified	Uncertain significance (Feb 28, 2024)
12-75501985-C-T		not specified	Uncertain significance (Jun 27, 2022)
12-75506341-A-G		not specified	Uncertain significance (Sep 14, 2023)
12-75506522-T-C		not specified	Uncertain significance (Mar 06, 2023)
12-75506616-CA-C			Benign (Dec 29, 2023)
12-75506616-C-CAAAAAAAA			Likely benign (Dec 20, 2023)
12-75506616-C-CAAAAAAAAAAA			Likely benign (Jan 01, 2023)
12-75506889-C-T		not specified	Uncertain significance (Nov 30, 2022)
12-75508416-C-A		not specified	Uncertain significance (Nov 03, 2023)
12-75508428-G-A		not specified	Uncertain significance (May 17, 2023)
12-75511533-T-C		not specified	Uncertain significance (Aug 04, 2022)
12-75511560-G-A		not specified	Uncertain significance (Jan 19, 2024)
12-75511579-C-G		not specified	Uncertain significance (Aug 08, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KRR1	protein_coding	protein_coding	ENST00000229214	10	14733

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000693	0.996	125497	0	230	125727	0.000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.522	172	192	0.894	0.00000920	2508
Missense in Polyphen		39	55.57	0.70182		769
Synonymous	-0.746	73	65.3	1.12	0.00000313	667
Loss of Function	2.54	9	21.8	0.413	0.00000118	283

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00644	0.00644
Ashkenazi Jewish	0.00	0.00
East Asian	0.00192	0.00169
Finnish	0.0000496	0.0000462
European (Non-Finnish)	0.000162	0.000158
Middle Eastern	0.00192	0.00169
South Asian	0.000290	0.000261
Other	0.000354	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for 40S ribosome biogenesis. Involved in nucleolar processing of pre-18S ribosomal RNA and ribosome assembly (By similarity). {ECO:0000250}.
• Pathway: rRNA processing;Metabolism of RNA;rRNA modification in the nucleus and cytosol;rRNA processing in the nucleus and cytosol (Consensus)

Recessive Scores

• pRec: 0.378

Intolerance Scores

• loftool: 0.788
• rvis_EVS: -0.29
• rvis_percentile_EVS: 33.2

Haploinsufficiency Scores

• pHI: 0.959
• hipred: Y
• hipred_score: 0.694
• ghis: 0.627

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.989

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Krr1

Gene ontology

• Biological process: rRNA processing
• Cellular component: nucleus;nucleoplasm;nucleolus;cytoplasm;membrane;small-subunit processome;intercellular bridge
• Molecular function: RNA binding;protein binding