KRBOX4

KRAB box domain containing 4

Basic information

Region (hg38): X:46447292-46497422

Previous symbols: [ "ZNF673" ]

Links

ENSG00000147121 ∙ NCBI:55634 ∙ OMIM:300585 ∙ HGNC:26007 ∙ Uniprot:Q5JUW0 ∙ 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 KRBOX4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KRBOX4 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			7	1		8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	1	0

Variants in KRBOX4

This is a list of pathogenic ClinVar variants found in the KRBOX4 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-46463210-C-T		not specified	Uncertain significance (Jan 26, 2023)
X-46463247-A-C		not specified	Uncertain significance (Jun 17, 2022)
X-46463282-G-A		not specified	Conflicting classifications of pathogenicity (Mar 20, 2024)
X-46471140-AGA-T			not provided (-)
X-46472758-C-G		not specified	Uncertain significance (Jan 22, 2024)
X-46472827-G-A		not specified	Uncertain significance (May 24, 2023)
X-46472840-T-C		not specified	Uncertain significance (Dec 03, 2024)
X-46472847-T-A		not specified	Uncertain significance (May 24, 2023)
X-46472872-T-G		not specified	Uncertain significance (Oct 09, 2024)
X-46472957-A-C		not specified	Uncertain significance (Nov 08, 2022)
X-46472965-T-C		not specified	Uncertain significance (Sep 27, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KRBOX4	protein_coding	protein_coding	ENST00000344302	4	50566

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.648	0.328	120960	0	1	120961	0.00000413

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.259	57	62.8	0.908	0.00000458	1129
Missense in Polyphen		12	12.934	0.92779		289
Synonymous	-0.528	29	25.6	1.13	0.00000208	299
Loss of Function	1.70	0	3.37	0.00	2.13e-7	59

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000730	0.0000553
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.0000730	0.0000553
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)

Recessive Scores

• pRec: 0.109

Intolerance Scores

• rvis_EVS: 0.44
• rvis_percentile_EVS: 77.45

Haploinsufficiency Scores

• pHI: 0.108
• hipred: N
• hipred_score: 0.172
• ghis: 0.437

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

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, DNA-templated
• Molecular function: nucleic acid binding