KLF13

KLF transcription factor 13, the group of Kruppel like factors|Zinc fingers C2H2-type

Basic information

Region (hg38): 15:31326835-31435665

Links

ENSG00000169926 ∙ NCBI:51621 ∙ OMIM:605328 ∙ HGNC:13672 ∙ Uniprot:Q9Y2Y9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• congenital heart disease (Moderate), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the KLF13 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KLF13 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				7	3	10
missense			28			28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	28	7	3

Variants in KLF13

This is a list of pathogenic ClinVar variants found in the KLF13 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-31327220-C-T		not specified	Uncertain significance (Apr 25, 2022)
15-31327239-C-T			Benign (Dec 31, 2019)
15-31327269-G-A			Likely benign (Jun 26, 2018)
15-31327301-G-A		not specified	Uncertain significance (Nov 13, 2023)
15-31327307-A-G		not specified	Uncertain significance (Jul 12, 2022)
15-31327315-C-G		not specified	Uncertain significance (Nov 08, 2022)
15-31327328-C-T		not specified	Uncertain significance (May 08, 2024)
15-31327339-A-C		not specified	Uncertain significance (Aug 04, 2021)
15-31327345-A-C		not specified	Uncertain significance (Nov 19, 2021)
15-31327408-C-T		not specified	Uncertain significance (Nov 22, 2023)
15-31327451-C-T		not specified	Uncertain significance (Jul 26, 2024)
15-31327493-C-T		not specified	Uncertain significance (Jun 10, 2024)
15-31327495-C-T		not specified	Uncertain significance (Feb 05, 2024)
15-31327501-C-G		not specified	Uncertain significance (May 17, 2023)
15-31327517-C-T		not specified	Uncertain significance (Jun 07, 2024)
15-31327524-G-C		not specified	Uncertain significance (Apr 25, 2022)
15-31327528-A-C		not specified	Uncertain significance (Jul 06, 2021)
15-31327531-T-C		not specified	Uncertain significance (Jul 06, 2021)
15-31327535-C-G		not specified	Uncertain significance (Oct 16, 2024)
15-31327537-G-C		not specified	Uncertain significance (Oct 05, 2021)
15-31327538-G-C		not specified	Uncertain significance (Aug 13, 2021)
15-31327540-G-C		not specified	Uncertain significance (Aug 13, 2021)
15-31327544-A-C		not specified	Uncertain significance (Aug 13, 2021)
15-31327545-A-C		not specified	Uncertain significance (Aug 13, 2021)
15-31327549-G-C		not specified	Uncertain significance (Sep 30, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KLF13	protein_coding	protein_coding	ENST00000307145	2	108811

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.404	0.561	120367	0	2	120369	0.00000831

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.02	52	112	0.464	0.00000800	1809
Missense in Polyphen		2	6.6478	0.30085		86
Synonymous	-0.457	54	49.9	1.08	0.00000386	605
Loss of Function	1.68	1	5.08	0.197	2.20e-7	82

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000661	0.0000661
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	0.0000328	0.0000328
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Represses transcription by binding to the BTE site, a GC-rich DNA element, in competition with the activator SP1. It also represses transcription by interacting with the corepressor Sin3A and HDAC1. Activates RANTES expression in T-cells. {ECO:0000269|PubMed:11477107}.

Haploinsufficiency Scores

• pHI: 0.897
• hipred: Y
• hipred_score: 0.713
• ghis: 0.557

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.493

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Klf13
• Phenotype: cellular phenotype; endocrine/exocrine gland phenotype; immune system phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;transcription by RNA polymerase II;negative regulation of cell population proliferation;negative regulation of erythrocyte differentiation;positive regulation of transcription by RNA polymerase II
• 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 activator activity, RNA polymerase II-specific;protein binding;metal ion binding