MEIS3

Meis homeobox 3, the group of TALE class homeoboxes and pseudogenes

Basic information

Region (hg38): 19:47403124-47419527

Links

ENSG00000105419 ∙ NCBI:56917 ∙ OMIM:619443 ∙ HGNC:29537 ∙ Uniprot:Q99687 ∙ 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 MEIS3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MEIS3 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					1	1
missense			34	3		37
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	34	3	1

Variants in MEIS3

This is a list of pathogenic ClinVar variants found in the MEIS3 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-47406900-C-T		not specified	Uncertain significance (Jun 21, 2023)
19-47406929-C-A		not specified	Uncertain significance (Dec 21, 2022)
19-47406965-C-A		not specified	Uncertain significance (Dec 16, 2023)
19-47407386-C-T		not specified	Uncertain significance (Dec 06, 2022)
19-47407467-G-A		not specified	Uncertain significance (Dec 14, 2021)
19-47407517-G-C		not specified	Uncertain significance (Dec 18, 2023)
19-47407562-C-T		not specified	Uncertain significance (Aug 16, 2021)
19-47409100-G-A		not specified	Uncertain significance (Aug 20, 2023)
19-47409118-C-G		not specified	Uncertain significance (Jul 30, 2023)
19-47409160-C-T		not specified	Uncertain significance (May 18, 2022)
19-47409169-T-C		not specified	Uncertain significance (Oct 26, 2022)
19-47409172-C-T		not specified	Uncertain significance (Jan 30, 2024)
19-47409178-C-T		not specified	Uncertain significance (Jan 08, 2024)
19-47409200-C-A		not specified	Uncertain significance (Feb 09, 2022)
19-47409232-G-A		not specified	Uncertain significance (Mar 27, 2023)
19-47409235-T-A		not specified	Uncertain significance (Aug 16, 2021)
19-47409456-C-T		not specified	Uncertain significance (Aug 03, 2022)
19-47409474-C-A		not specified	Uncertain significance (Sep 27, 2022)
19-47409503-A-T		not specified	Uncertain significance (Nov 09, 2023)
19-47409508-C-G		not specified	Uncertain significance (Sep 15, 2021)
19-47414719-G-C		not specified	Uncertain significance (Oct 17, 2023)
19-47414755-C-T		not specified	Uncertain significance (Jul 14, 2021)
19-47414773-C-T		not specified	Likely benign (Sep 17, 2021)
19-47414800-C-T		not specified	Uncertain significance (Mar 19, 2024)
19-47414835-C-T		not specified	Uncertain significance (Jun 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MEIS3	protein_coding	protein_coding	ENST00000561293	12	16400

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.80e-9	0.789	125698	0	50	125748	0.000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.165	243	250	0.971	0.0000138	2704
Missense in Polyphen		65	74.867	0.8682		886
Synonymous	-0.544	113	106	1.07	0.00000643	842
Loss of Function	1.53	17	25.3	0.672	0.00000140	260

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000302	0.000297
Ashkenazi Jewish	0.0000997	0.0000992
East Asian	0.000326	0.000326
Finnish	0.00	0.00
European (Non-Finnish)	0.000169	0.000167
Middle Eastern	0.000326	0.000326
South Asian	0.000472	0.000457
Other	0.000334	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcriptional regulator which directly modulates PDPK1 expression, thus promoting survival of pancreatic beta-cells. Also regulates expression of NDFIP1, BNIP3, and CCNG1. {ECO:0000250|UniProtKB:P97368}.

Intolerance Scores

• loftool: 0.154
• rvis_EVS: -0.13
• rvis_percentile_EVS: 43.91

Haploinsufficiency Scores

• pHI: 0.185
• hipred: N
• hipred_score: 0.318
• ghis: 0.530

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Meis3

Gene ontology

• Biological process: positive regulation of transcription by RNA polymerase II;positive regulation of protein kinase B signaling;negative regulation of apoptotic signaling pathway
• Cellular component: nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific;chromatin binding;sequence-specific DNA binding