RUNX1T1

RUNX1 partner transcriptional co-repressor 1, the group of Zinc fingers MYND-type

Basic information

Region (hg38): 8:91954972-92103385

Previous symbols: [ "AML1T1", "CBFA2T1" ]

Links

ENSG00000079102 ∙ NCBI:862 ∙ OMIM:133435 ∙ HGNC:1535 ∙ Uniprot:Q06455 ∙ 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 RUNX1T1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RUNX1T1 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						0
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	1	0	0

Variants in RUNX1T1

This is a list of pathogenic ClinVar variants found in the RUNX1T1 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-91960318-A-G		not specified	Uncertain significance (Aug 08, 2023)
8-91960320-C-T		RUNX1T1-related disorder	Likely benign (Apr 10, 2019)
8-91960491-C-T		RUNX1T1-related disorder	Benign (May 08, 2018)
8-91970724-G-A		RUNX1T1-related disorder	Likely benign (Apr 08, 2019)
8-91970768-C-T		not specified	Uncertain significance (Oct 04, 2022)
8-91970796-G-A			Likely benign (May 30, 2018)
8-91970841-G-A			Benign (Dec 31, 2019)
8-91975960-T-A		not specified	Uncertain significance (Oct 03, 2022)
8-91975978-G-GA		RUNX1T1-related disorder	Likely benign (Jul 31, 2019)
8-91986184-C-T		not specified	Likely benign (May 23, 2023)
8-91986222-C-T		not specified	Uncertain significance (Sep 01, 2021)
8-91986238-A-G		RUNX1T1-related disorder	Benign (Jun 16, 2018)
8-91986880-G-A		RUNX1T1-related disorder	Benign (Dec 31, 2019)
8-91991641-A-G		not specified	Uncertain significance (May 10, 2022)
8-91991789-C-T		not specified	Uncertain significance (Apr 06, 2022)
8-91991790-G-A		RUNX1T1-related disorder	Benign (Aug 14, 2019)
8-91991802-G-A		RUNX1T1-related disorder	Benign (Jul 02, 2018)
8-91991855-G-A		not specified	Uncertain significance (Dec 12, 2023)
8-92005138-C-A		not specified	Uncertain significance (Apr 28, 2022)
8-92005141-T-G		not specified	Uncertain significance (Dec 27, 2022)
8-92005163-C-G		not specified	Uncertain significance (Jul 21, 2022)
8-92005259-G-A		RUNX1T1-related disorder	Likely benign (Jun 13, 2019)
8-92014582-T-C		RUNX1T1-related disorder	Benign (Dec 31, 2019)
8-92014681-T-G		not specified	Uncertain significance (Mar 24, 2023)
8-92014728-A-T		not specified	Uncertain significance (Aug 21, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RUNX1T1	protein_coding	protein_coding	ENST00000436581	11	148312

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.978	0.0223	125673	0	2	125675	0.00000796

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.17	255	373	0.684	0.0000228	4009
Missense in Polyphen		42	101.94	0.412		1055
Synonymous	-0.0891	151	150	1.01	0.00000968	1240
Loss of Function	4.33	4	29.3	0.137	0.00000157	327

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)	0.0000178	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcriptional corepressor which facilitates transcriptional repression via its association with DNA-binding transcription factors and recruitment of other corepressors and histone-modifying enzymes (PubMed:12559562, PubMed:15203199). Can repress the expression of MMP7 in a ZBTB33-dependent manner (PubMed:23251453). Can repress transactivation mediated by TCF12 (PubMed:16803958). Acts as a negative regulator of adipogenesis (By similarity). The AML1-MTG8/ETO fusion protein frequently found in leukemic cells is involved in leukemogenesis and contributes to hematopoietic stem/progenitor cell self-renewal (PubMed:23812588). {ECO:0000250|UniProtKB:Q61909, ECO:0000269|PubMed:10973986, ECO:0000269|PubMed:16803958, ECO:0000269|PubMed:23251453, ECO:0000269|PubMed:23812588, ECO:0000303|PubMed:12559562, ECO:0000303|PubMed:15203199}.
• Disease: DISEASE: Note=A chromosomal aberration involving RUNX1T1 is a cause of acute myeloid leukemia (AML-M2). Translocation t(8;21)(q22;q22) with RUNX1/AML1. {ECO:0000269|PubMed:1423235, ECO:0000269|PubMed:7541640, ECO:0000269|PubMed:8334990, ECO:0000269|PubMed:8353289}.
• Pathway: Acute myeloid leukemia - Homo sapiens (human);Pathways in cancer - Homo sapiens (human);Transcriptional misregulation in cancer - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.589

Intolerance Scores

• loftool: 0.310
• rvis_EVS: -1
• rvis_percentile_EVS: 8.32

Haploinsufficiency Scores

• pHI: 0.851
• hipred: Y
• hipred_score: 0.853
• ghis: 0.645

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.685

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Runx1t1
• Phenotype: integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; digestive/alimentary phenotype; reproductive system phenotype; normal phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: generation of precursor metabolites and energy;negative regulation of fat cell differentiation;negative regulation of transcription, DNA-templated
• Cellular component: nucleus;nucleoplasm;nuclear matrix
• Molecular function: DNA binding;DNA-binding transcription factor activity;transcription corepressor activity;protein binding;metal ion binding