KBTBD12

kelch repeat and BTB domain containing 12, the group of BTB domain containing

Basic information

Region (hg38): 3:127915232-127987671

Previous symbols: [ "KLHDC6" ]

Links

ENSG00000187715 ∙ NCBI:166348 ∙ ∙ HGNC:25731 ∙ Uniprot:Q3ZCT8 ∙ 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 KBTBD12 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KBTBD12 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			38	1		39
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	39	1	0

Variants in KBTBD12

This is a list of pathogenic ClinVar variants found in the KBTBD12 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-127923083-A-G		not specified	Uncertain significance (Jan 03, 2024)
3-127923143-G-A		not specified	Uncertain significance (Aug 04, 2021)
3-127923158-G-A		not specified	Uncertain significance (Aug 02, 2022)
3-127923186-T-G		not specified	Uncertain significance (Aug 20, 2024)
3-127923215-T-G		not specified	Uncertain significance (May 01, 2024)
3-127923284-T-C		not specified	Likely benign (Sep 20, 2023)
3-127923309-C-T		not specified	Uncertain significance (Oct 12, 2024)
3-127923360-A-C		not specified	Uncertain significance (Dec 15, 2023)
3-127923468-T-C		not specified	Uncertain significance (Mar 16, 2022)
3-127923499-A-C		not specified	Uncertain significance (Jul 19, 2023)
3-127923522-A-C		not specified	Uncertain significance (Nov 09, 2023)
3-127923531-A-G		not specified	Uncertain significance (Jan 03, 2024)
3-127923600-T-A		not specified	Uncertain significance (May 25, 2022)
3-127923603-T-C		not specified	Uncertain significance (May 06, 2024)
3-127923625-A-G		not specified	Uncertain significance (Nov 15, 2024)
3-127923686-C-T		not specified	Uncertain significance (Jun 28, 2024)
3-127923738-A-C		not specified	Uncertain significance (Sep 13, 2023)
3-127923777-T-G		not specified	Uncertain significance (Nov 12, 2024)
3-127923795-A-T		not specified	Uncertain significance (Jan 23, 2023)
3-127923806-A-G		not specified	Uncertain significance (Aug 04, 2021)
3-127923861-T-C		not specified	Uncertain significance (Jun 05, 2024)
3-127923912-C-T		not specified	Uncertain significance (Nov 25, 2024)
3-127923936-G-A		not specified	Uncertain significance (Nov 23, 2024)
3-127923977-C-T		not specified	Uncertain significance (Apr 26, 2024)
3-127923987-A-G		not specified	Uncertain significance (Sep 25, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KBTBD12	protein_coding	protein_coding	ENST00000405109	5	72440

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.34e-14	0.0632	125325	1	267	125593	0.00107

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.277	316	330	0.957	0.0000162	4106
Missense in Polyphen		120	129.7	0.92521		1550
Synonymous	1.01	103	117	0.881	0.00000566	1155
Loss of Function	0.618	23	26.4	0.870	0.00000153	322

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00580	0.00569
Ashkenazi Jewish	0.00	0.00
East Asian	0.00342	0.00332
Finnish	0.000476	0.000462
European (Non-Finnish)	0.000493	0.000485
Middle Eastern	0.00342	0.00332
South Asian	0.000980	0.000882
Other	0.000837	0.000816

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0921

Intolerance Scores

• loftool: 0.723
• rvis_EVS: -0.11
• rvis_percentile_EVS: 45.36

Haploinsufficiency Scores

• pHI: 0.0797
• hipred: N
• hipred_score: 0.219
• ghis: 0.505

Essentials

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

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Kbtbd12