KRBA2

KRAB-A domain containing 2

Basic information

Region (hg38): 17:8356902-8376704

Links

ENSG00000184619 ∙ NCBI:124751 ∙ ∙ HGNC:26989 ∙ Uniprot:Q6ZNG9 ∙ 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 KRBA2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KRBA2 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			19	2		21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	2	0

Variants in KRBA2

This is a list of pathogenic ClinVar variants found in the KRBA2 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-8369184-C-T		not specified	Uncertain significance (Oct 25, 2023)
17-8369212-C-A		not specified	Uncertain significance (Aug 09, 2021)
17-8369299-C-G		not specified	Uncertain significance (Mar 11, 2024)
17-8369372-T-C		not specified	Likely benign (Apr 25, 2022)
17-8369382-T-C		not specified	Uncertain significance (Oct 30, 2024)
17-8369415-C-T		not specified	Uncertain significance (May 12, 2024)
17-8369434-C-T		not specified	Uncertain significance (Mar 04, 2024)
17-8369456-T-G		not specified	Uncertain significance (Oct 04, 2022)
17-8369465-T-A		not specified	Uncertain significance (Jun 25, 2024)
17-8369475-G-A		not specified	Likely benign (Aug 17, 2021)
17-8369516-C-T		not specified	Likely benign (Nov 09, 2024)
17-8369519-C-G		not specified	Uncertain significance (Aug 19, 2024)
17-8369571-C-T		not specified	Uncertain significance (Dec 02, 2022)
17-8369573-A-G		not specified	Uncertain significance (Dec 17, 2023)
17-8369575-C-G		not specified	Uncertain significance (Jun 05, 2024)
17-8369583-C-T		not specified	Uncertain significance (Jul 23, 2024)
17-8369631-C-T		not specified	Likely benign (Jun 16, 2024)
17-8369790-C-A		not specified	Uncertain significance (Oct 27, 2022)
17-8369856-G-C		not specified	Uncertain significance (Nov 08, 2022)
17-8369942-G-T		not specified	Uncertain significance (Nov 25, 2024)
17-8369978-A-T		not specified	Uncertain significance (Jan 18, 2022)
17-8369996-T-C		not specified	Uncertain significance (Aug 04, 2023)
17-8370002-A-G		not specified	Uncertain significance (Oct 26, 2021)
17-8370047-T-C		not specified	Uncertain significance (Jul 05, 2024)
17-8370056-T-C		not specified	Uncertain significance (May 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KRBA2	protein_coding	protein_coding	ENST00000331336	2	8075

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.88e-7	0.442	125482	2	264	125748	0.00106

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.456	246	267	0.921	0.0000140	3268
Missense in Polyphen		46	45.411	1.013		701
Synonymous	1.80	73	95.4	0.765	0.00000486	916
Loss of Function	0.769	12	15.2	0.787	7.98e-7	191

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00262	0.00262
Ashkenazi Jewish	0.00	0.00
East Asian	0.00680	0.00665
Finnish	0.00	0.00
European (Non-Finnish)	0.000159	0.000158
Middle Eastern	0.00680	0.00665
South Asian	0.00123	0.00121
Other	0.000652	0.000652

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.911
• rvis_EVS: 0.04
• rvis_percentile_EVS: 57.31

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.112
• ghis: 0.461

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0290

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;DNA integration
• Molecular function: nucleic acid binding