KLF17

KLF transcription factor 17, the group of Kruppel like factors|Zinc fingers C2H2-type

Basic information

Region (hg38): 1:44118821-44135140

Previous symbols: [ "ZNF393" ]

Links

ENSG00000171872 ∙ NCBI:128209 ∙ OMIM:609602 ∙ HGNC:18830 ∙ Uniprot:Q5JT82 ∙ 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 KLF17 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KLF17 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			26	4		30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	4	0

Variants in KLF17

This is a list of pathogenic ClinVar variants found in the KLF17 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-44118969-C-T		not specified	Likely benign (Mar 23, 2023)
1-44129359-G-A		EBV-positive nodal T- and NK-cell lymphoma	Likely benign (-)
1-44129369-C-T		not specified	Uncertain significance (Dec 20, 2023)
1-44129396-C-A		not specified	Uncertain significance (Aug 05, 2023)
1-44129438-C-A		not specified	Uncertain significance (Mar 04, 2024)
1-44129472-G-T		not specified	Uncertain significance (May 18, 2022)
1-44129531-C-A		not specified	Uncertain significance (Sep 14, 2023)
1-44129540-G-T		not specified	Uncertain significance (Jan 12, 2024)
1-44129549-T-C		not specified	Uncertain significance (Dec 30, 2023)
1-44129552-C-T		not specified	Uncertain significance (Dec 16, 2021)
1-44129582-C-T		not specified	Likely benign (Feb 17, 2022)
1-44129618-G-C		not specified	Uncertain significance (May 30, 2024)
1-44129644-A-G		not specified	Uncertain significance (Apr 17, 2023)
1-44129704-A-G		not specified	Uncertain significance (Jun 17, 2024)
1-44129708-C-T		not specified	Uncertain significance (Jan 09, 2023)
1-44129731-C-T		not specified	Uncertain significance (Aug 17, 2022)
1-44129735-C-G		not specified	Uncertain significance (Jun 27, 2022)
1-44129809-C-A		not specified	Uncertain significance (May 08, 2024)
1-44129810-C-T		not specified	Uncertain significance (Feb 27, 2023)
1-44129839-A-T		not specified	Uncertain significance (Feb 05, 2024)
1-44129965-G-T		not specified	Uncertain significance (Jan 13, 2023)
1-44129981-A-G		not specified	Uncertain significance (Jun 11, 2024)
1-44129986-C-T		not specified	Likely benign (Oct 26, 2021)
1-44130003-C-A		not specified	Uncertain significance (Oct 06, 2022)
1-44130028-G-C		not specified	Uncertain significance (May 12, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KLF17	protein_coding	protein_coding	ENST00000372299	3	16291

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.66e-9	0.214	125706	0	41	125747	0.000163

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.125	239	234	1.02	0.0000138	2533
Missense in Polyphen		47	51.487	0.91285		606
Synonymous	-0.369	94	89.6	1.05	0.00000540	789
Loss of Function	0.488	14	16.1	0.869	9.35e-7	160

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000867	0.0000867
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000229	0.000229
Middle Eastern	0.00	0.00
South Asian	0.000392	0.000392
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcription repressor that binds to the promoter of target genes and prevents their expression. Acts as a negative regulator of epithelial-mesenchymal transition and metastasis in breast cancer. Specifically binds the 5'-CACCC-3' sequence in the promoter of ID1, a key metastasis regulator in breast cancer, and repress its expression. May be a germ cell-specific transcription factor that plays important roles in spermatid differentiation and oocyte development (By similarity). {ECO:0000250, ECO:0000269|PubMed:16460907}.

Recessive Scores

• pRec: 0.0701

Intolerance Scores

• loftool: 0.860
• rvis_EVS: 0.07
• rvis_percentile_EVS: 58.96

Haploinsufficiency Scores

• pHI: 0.0479
• hipred: N
• hipred_score: 0.123
• ghis: 0.377

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0141

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Klf17

Zebrafish Information Network

• Gene name: klf17
• Affected structure: nucleate erythrocyte
• Phenotype tag: abnormal
• Phenotype quality: absent

Gene ontology

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