KLF12

KLF transcription factor 12, the group of Kruppel like factors|Zinc fingers C2H2-type

Basic information

Region (hg38): 13:73686088-74134404

Links

ENSG00000118922 ∙ NCBI:11278 ∙ OMIM:607531 ∙ HGNC:6346 ∙ Uniprot:Q9Y4X4 ∙ 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 KLF12 gene.

• Inborn genetic diseases (10 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KLF12 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			10			10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	0	0

Variants in KLF12

This is a list of pathogenic ClinVar variants found in the KLF12 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-73715451-C-T		not specified	Uncertain significance (Nov 09, 2021)
13-73715473-A-G		not specified	Uncertain significance (Feb 28, 2023)
13-73715482-G-A		not specified	Uncertain significance (Dec 16, 2023)
13-73813213-T-A		not specified	Uncertain significance (Dec 14, 2023)
13-73813218-T-C		not specified	Uncertain significance (Sep 16, 2021)
13-73813270-C-T		not specified	Uncertain significance (May 26, 2022)
13-73846000-G-C		not specified	Uncertain significance (Mar 16, 2022)
13-73846073-C-T		not specified	Uncertain significance (Oct 05, 2023)
13-73846079-A-T		not specified	Uncertain significance (Oct 14, 2023)
13-73846126-G-A		not specified	Uncertain significance (Oct 12, 2021)
13-73846133-G-A		not specified	Uncertain significance (Mar 07, 2023)
13-73846141-G-A		not specified	Uncertain significance (Dec 19, 2022)
13-73846307-C-T		not specified	Uncertain significance (Jun 30, 2023)
13-73943984-T-G		not specified	Uncertain significance (Aug 22, 2023)
13-73944015-C-A		not specified	Uncertain significance (Jun 30, 2023)
13-73944051-T-C		not specified	Uncertain significance (Sep 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KLF12	protein_coding	protein_coding	ENST00000377669	7	448169

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.981	0.0193	125697	0	2	125699	0.00000796

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.79	167	246	0.678	0.0000150	2582
Missense in Polyphen		56	108.93	0.51409		1117
Synonymous	-0.641	109	101	1.08	0.00000657	839
Loss of Function	3.53	1	16.5	0.0608	7.60e-7	214

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)	0.0000176	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Confers strong transcriptional repression to the AP-2- alpha gene. Binds to a regulatory element (A32) in the AP-2-alpha gene promoter.

Recessive Scores

• pRec: 0.116

Intolerance Scores

• loftool: 0.0700
• rvis_EVS: -0.49
• rvis_percentile_EVS: 22.36

Haploinsufficiency Scores

• pHI: 0.864
• hipred: Y
• hipred_score: 0.739
• ghis: 0.584

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• gene_indispensability_pred: E
• gene_indispensability_score: 0.942

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Klf12

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;regulation of transcription by RNA polymerase II;positive regulation of transcription by RNA polymerase II
• Cellular component: nucleus;nucleoplasm;cytosol
• Molecular function: RNA polymerase II regulatory region sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription repressor activity, RNA polymerase II-specific;DNA binding;DNA-binding transcription factor activity;transcription corepressor activity;protein binding;metal ion binding