BMP2K

BMP2 inducible kinase, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): 4:78776341-78916365

Links

ENSG00000138756 ∙ NCBI:55589 ∙ OMIM:617648 ∙ HGNC:18041 ∙ Uniprot:Q9NSY1 ∙ 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 BMP2K gene.

• Inborn genetic diseases (27 variants)
• not specified (1 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BMP2K 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			25	2		27
nonsense				1		1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	25	3	0

Variants in BMP2K

This is a list of pathogenic ClinVar variants found in the BMP2K region.

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

Position	Type	Phenotype	Significance	ClinVar
4-78776602-G-C		not specified	Uncertain significance (Jul 17, 2023)
4-78776614-G-A		not specified	Uncertain significance (Apr 06, 2022)
4-78776641-G-C		not specified	Uncertain significance (Oct 17, 2023)
4-78776692-A-C		not specified	Uncertain significance (Oct 22, 2021)
4-78826108-A-G		not specified	Uncertain significance (May 31, 2023)
4-78826150-A-G		not specified	Uncertain significance (Dec 21, 2022)
4-78833624-T-A		not specified	Uncertain significance (Mar 01, 2023)
4-78833660-G-A		not specified	Uncertain significance (Nov 21, 2022)
4-78842424-C-T		not specified	Uncertain significance (Aug 02, 2023)
4-78842478-T-C		not specified	Uncertain significance (Jan 19, 2024)
4-78842504-C-A		not specified	Uncertain significance (Dec 18, 2023)
4-78847205-A-G		not specified	Uncertain significance (Sep 06, 2022)
4-78847265-T-C		not specified	Uncertain significance (Apr 04, 2023)
4-78851003-A-G		not specified	Likely benign (Apr 26, 2023)
4-78851026-C-T		not specified	Uncertain significance (Mar 01, 2023)
4-78851038-A-T		not specified	Uncertain significance (Feb 05, 2024)
4-78859605-C-T		not specified	Uncertain significance (Mar 01, 2024)
4-78861398-A-G		not specified	Uncertain significance (Mar 22, 2023)
4-78861420-C-T		not specified	Uncertain significance (Jul 12, 2023)
4-78865591-A-G		not specified	Uncertain significance (Mar 08, 2024)
4-78865649-T-G		not specified	Uncertain significance (Aug 16, 2021)
4-78870836-C-A		not specified	Uncertain significance (Dec 07, 2021)
4-78870921-A-G		not specified	Uncertain significance (Feb 27, 2024)
4-78870926-C-G		not specified	Uncertain significance (Mar 01, 2024)
4-78870927-A-T		not specified	Uncertain significance (Mar 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BMP2K	protein_coding	protein_coding	ENST00000335016	16	140031

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.219	0.781	125695	0	53	125748	0.000211

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.402	556	583	0.953	0.0000294	7658
Missense in Polyphen		72	97.088	0.7416		1296
Synonymous	0.155	207	210	0.986	0.0000106	2191
Loss of Function	5.07	12	51.1	0.235	0.00000250	619

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000375	0.000367
Ashkenazi Jewish	0.00	0.00
East Asian	0.00131	0.00120
Finnish	0.0000465	0.0000462
European (Non-Finnish)	0.000143	0.000132
Middle Eastern	0.00131	0.00120
South Asian	0.000203	0.000196
Other	0.000166	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in osteoblast differentiation.
• Pathway: Transcriptional misregulation in cancer - Homo sapiens (human) (Consensus)

Intolerance Scores

• loftool: 0.554
• rvis_EVS: 0.27
• rvis_percentile_EVS: 70.75

Haploinsufficiency Scores

• pHI: 0.781
• hipred: N
• hipred_score: 0.414
• ghis: 0.470

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.892

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Bmp2k
• Phenotype: vision/eye phenotype

Gene ontology

• Biological process: protein phosphorylation;regulation of endocytosis;regulation of bone mineralization;regulation of catalytic activity
• Cellular component: nucleus;nuclear speck
• Molecular function: protein serine/threonine kinase activity;ATP binding;phosphatase regulator activity