KRR1

protein-coding

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

Gene summary

Enables RNA binding activity. Involved in ribosomal small subunit biogenesis. Located in nucleolus and nucleoplasm. Part of small-subunit processome. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

HRB2

MANE transcript

NM_007043.7

Inheritance

—

ClinVar variants

U:53B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.41

Max pathogenic AF

—

Genomic locus

chr12:75,490,863-75,511,636

External References & Databases

Ensembl (ENSG00000111615)

Transcript & Mutation Effects

hg38 • Region Span ~20.8 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to KRR1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 49

not providedTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_007043.7. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			48 clinvar	3 clinvar		51
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			5 clinvar			5
Total	0	0	53	3	0	56

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 19 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_007043.7	RefSeq	NP_008974.5	10	MANE Select
ENST00000229214.9	Ensembl	ENSP00000229214.4	10	MANE Select
ENST00000438169.6	Ensembl	ENSP00000411740.2	9	Standard
ENST00000907976.1	Ensembl	ENSP00000578035.1	10	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

rRNA processing
Metabolism of RNA
rRNA modification in the nucleus and cytosol
rRNA processing in the nucleus and cytosol

Biological Process

rRNA processing

Molecular Function

RNA binding
protein binding

Cellular Component

nucleus
nucleoplasm
nucleolus
cytoplasm
membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000229214
Coding exons: 10
Length: 14733
Individuals with no LoFs: 125497
Homozygous LoFs: 0
Heterozygous LoFs: 230
Defined: 125727
p: 0.000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.522	172	192	0.894	0.00000920	2508
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00037	0.00037	rare
Latino/Admixed American	0.0061	0.0048	notable
Ashkenazi Jewish	0	0.0	absent
East Asian	0.0019	0.0017	notable
Finnish	0.000050	0.000046	rare
European (Non-Finnish)	0.00016	0.00016	rare
South Asian	0.00029	0.00026	rare
Other	0.00035	0.00033	rare

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.378

Intolerance Scores

LoFtool: 0.788
RVIS EVS: -0.29
RVIS percentile EVS: 33.2

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.989

Gene Damage Prediction

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