KLF16

KLF transcription factor 16, the group of Kruppel like factors|Zinc fingers C2H2-type

Basic information

Region (hg38): 19:1852398-1863579

Links

ENSG00000129911 ∙ NCBI:83855 ∙ OMIM:606139 ∙ HGNC:16857 ∙ Uniprot:Q9BXK1 ∙ 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 KLF16 gene.

• Inborn genetic diseases (17 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KLF16 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			17			17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	0	0

Variants in KLF16

This is a list of pathogenic ClinVar variants found in the KLF16 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-1854484-G-C		not specified	Uncertain significance (Sep 14, 2023)
19-1854536-T-G		not specified	Uncertain significance (Jan 24, 2023)
19-1854554-C-T		not specified	Uncertain significance (Dec 06, 2022)
19-1854563-G-A		not specified	Uncertain significance (Oct 10, 2023)
19-1854725-C-G		not specified	Uncertain significance (Apr 20, 2023)
19-1863076-G-A		not specified	Uncertain significance (Mar 27, 2023)
19-1863082-T-C		not specified	Uncertain significance (Feb 21, 2024)
19-1863133-G-A		not specified	Uncertain significance (Sep 30, 2021)
19-1863139-G-A		not specified	Uncertain significance (Oct 03, 2022)
19-1863140-G-C		not specified	Uncertain significance (Jul 12, 2023)
19-1863158-G-T		not specified	Uncertain significance (Mar 20, 2023)
19-1863175-G-C		not specified	Uncertain significance (Jan 18, 2022)
19-1863179-C-A		not specified	Uncertain significance (May 27, 2022)
19-1863188-A-G		not specified	Uncertain significance (Nov 10, 2021)
19-1863241-T-G		not specified	Uncertain significance (Oct 26, 2021)
19-1863253-C-G		not specified	Uncertain significance (Aug 20, 2023)
19-1863268-T-G		not specified	Uncertain significance (Nov 16, 2021)
19-1863394-G-A		not specified	Uncertain significance (Apr 20, 2023)
19-1863407-C-T		not specified	Uncertain significance (Feb 23, 2023)
19-1863437-A-C		not specified	Uncertain significance (Nov 10, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KLF16	protein_coding	protein_coding	ENST00000250916	2	11169

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.195	0.659	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.50	46	85.0	0.541	0.00000601	1537
Missense in Polyphen		22	47.683	0.46138		450
Synonymous	-0.695	40	34.8	1.15	0.00000235	587
Loss of Function	0.961	1	2.71	0.369	1.14e-7	52

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

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcription factor that binds GC and GT boxes and displaces Sp1 and Sp3 from these sequences. Modulates dopaminergic transmission in the brain (By similarity). {ECO:0000250}.

Haploinsufficiency Scores

• pHI: 0.312
• hipred: Y
• hipred_score: 0.506
• ghis: 0.638

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 0.686

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Klf16

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;regulation of transcription by RNA polymerase II;dopamine receptor signaling pathway
• Cellular component: nucleus
• Molecular function: RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription repressor activity, RNA polymerase II-specific;metal ion binding