KRBOX1

KRAB box domain containing 1

Basic information

Region (hg38): 3:42936385-42942792

Links

ENSG00000240747 ∙ NCBI:100506243 ∙ ∙ HGNC:38708 ∙ Uniprot:C9JBD0 ∙ 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 KRBOX1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KRBOX1 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			4	2		6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	4	2	0

Variants in KRBOX1

This is a list of pathogenic ClinVar variants found in the KRBOX1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-42941283-A-G		not specified	Uncertain significance (Mar 25, 2024)
3-42941308-A-G		not specified	Uncertain significance (Aug 13, 2021)
3-42941973-A-G		not specified	Uncertain significance (Aug 29, 2023)
3-42941975-C-T		not specified	Uncertain significance (Mar 08, 2024)
3-42941984-G-A		not specified	Likely benign (Jun 27, 2022)
3-42942065-T-C		not specified	Uncertain significance (Jul 11, 2023)
3-42942610-G-A		not specified	Likely benign (Aug 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KRBOX1	protein_coding	protein_coding	ENST00000418176	4	133310

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0176	0.736	109694	0	1	109695	0.00000456

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.674	44	58.5	0.752	0.00000286	808
Missense in Polyphen		10	12.72	0.78616		183
Synonymous	1.21	15	22.3	0.673	0.00000120	239
Loss of Function	0.763	3	4.80	0.624	2.02e-7	64

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.0000356	0.0000356
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.112
• ghis: 0.458

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Gene ontology

• Biological process: regulation of transcription, DNA-templated
• Cellular component: nucleus
• Molecular function: nucleic acid binding