KRBOX5

KRAB box domain containing 5

Basic information

Region (hg38): 16:31713229-31794869

Previous symbols: [ "ZNF720" ]

Links

ENSG00000197302 ∙ NCBI:124411 ∙ ∙ HGNC:26987 ∙ Uniprot:Q7Z2F6 ∙ 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 KRBOX5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KRBOX5 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			6	1		7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	1	0

Variants in KRBOX5

This is a list of pathogenic ClinVar variants found in the KRBOX5 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-31722665-C-T		not specified	Uncertain significance (Jun 05, 2024)
16-31722666-G-A		not specified	Likely benign (Oct 12, 2021)
16-31722680-C-T		not specified	Uncertain significance (Apr 08, 2024)
16-31722708-A-G		not specified	Uncertain significance (Jan 26, 2023)
16-31723261-T-C		not specified	Uncertain significance (Apr 24, 2023)
16-31723266-G-C		not specified	Uncertain significance (Dec 02, 2022)
16-31753778-A-G		not specified	Uncertain significance (Nov 13, 2023)
16-31753790-G-T		not specified	Uncertain significance (Sep 25, 2023)
16-31753826-A-C		not specified	Uncertain significance (Oct 01, 2024)
16-31753895-G-T		not specified	Uncertain significance (Nov 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KRBOX5	protein_coding	protein_coding	ENST00000316491	5	81641

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.217	0.749	125231	0	5	125236	0.0000200

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.491	49	59.7	0.821	0.00000291	816
Missense in Polyphen		7	16.753	0.41783		250
Synonymous	0.760	19	23.7	0.801	0.00000126	220
Loss of Function	1.76	2	7.06	0.283	2.97e-7	95

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.000219	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000269	0.0000265
Middle Eastern	0.000219	0.000109
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription (Consensus)

Intolerance Scores

• rvis_EVS: 0.59
• rvis_percentile_EVS: 82.37

Haploinsufficiency Scores

• pHI: 0.0690
• hipred: N
• hipred_score: 0.148

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.734

Gene Damage Prediction

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

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;nucleic acid binding