BMS1

BMS1 ribosome biogenesis factor, the group of SSU processome

Basic information

Region (hg38): 10:42782794-42834937

Previous symbols: [ "BMS1L" ]

Links

ENSG00000165733 ∙ NCBI:9790 ∙ OMIM:611448 ∙ HGNC:23505 ∙ Uniprot:Q14692 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• aplasia cutis congenita (Limited), mode of inheritance: AD
• aplasia cutis congenita (Supportive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Aplasia cutis congenita, nonsyndromic	AD	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Dermatologic	23785305

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the BMS1 gene.

• Inborn genetic diseases (48 variants)
• not provided (37 variants)
• Aplasia cutis congenita (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BMS1 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				12	7	19
missense			48	6	9	63
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding				3		3
Total	0	0	48	21	16

Variants in BMS1

This is a list of pathogenic ClinVar variants found in the BMS1 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-42784454-G-T		not specified	Uncertain significance (Nov 12, 2021)
10-42784457-A-G			Likely benign (Nov 20, 2017)
10-42784480-T-G		not specified	Uncertain significance (Nov 14, 2023)
10-42784506-C-T			Benign (Dec 31, 2019)
10-42784508-G-A			Likely benign (May 24, 2018)
10-42784538-G-A			Likely benign (Jan 12, 2018)
10-42784548-C-T		not specified	Uncertain significance (Nov 08, 2022)
10-42785504-A-G		not specified	Uncertain significance (Apr 12, 2022)
10-42785556-T-C		not specified	Uncertain significance (Dec 05, 2022)
10-42785565-T-C		BMS1-related disorder	Likely benign (Jun 12, 2019)
10-42785621-T-C			Likely benign (Dec 31, 2019)
10-42785628-G-A		not specified	Uncertain significance (Mar 06, 2023)
10-42785661-C-T		not specified	Uncertain significance (Nov 13, 2023)
10-42787176-C-T		not specified	Uncertain significance (Jun 18, 2021)
10-42787177-G-A		not specified	Uncertain significance (Oct 04, 2022)
10-42790324-T-C		not specified	Uncertain significance (Nov 14, 2023)
10-42790391-A-C		not specified	Uncertain significance (Mar 15, 2023)
10-42790434-G-A		not specified	Uncertain significance (May 27, 2022)
10-42790506-T-C		not specified	Uncertain significance (Dec 03, 2021)
10-42790521-G-T			Likely benign (Jan 09, 2018)
10-42791631-C-T		BMS1-related disorder	Benign/Likely benign (Jun 12, 2020)
10-42791700-G-A		BMS1-related disorder	Benign (Dec 31, 2019)
10-42791727-C-T		BMS1-related disorder	Likely benign (Jun 12, 2020)
10-42791761-G-T			Likely benign (Feb 01, 2024)
10-42791776-T-A		BMS1-related disorder	Likely benign (Oct 31, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BMS1	protein_coding	protein_coding	ENST00000374518	22	52137

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000175	1.00	125698	0	50	125748	0.000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.260	676	695	0.972	0.0000371	8498
Missense in Polyphen		184	224.15	0.82088		2827
Synonymous	-1.34	276	249	1.11	0.0000137	2311
Loss of Function	5.08	19	62.2	0.305	0.00000346	758

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000349	0.000336
Ashkenazi Jewish	0.00	0.00
East Asian	0.000113	0.000109
Finnish	0.0000946	0.0000924
European (Non-Finnish)	0.000251	0.000246
Middle Eastern	0.000113	0.000109
South Asian	0.000371	0.000359
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May act as a molecular switch during maturation of the 40S ribosomal subunit in the nucleolus. {ECO:0000250|UniProtKB:Q08965}.
• Disease: DISEASE: Aplasia cutis congenita, non-syndromic (ACC) [MIM:107600]: A disorder characterized by congenital absence of a portion of skin in a localized or widespread area of the body. The lesions are most commonly localized on the scalp, however aplasia cutis congenita can affect any part of the body. {ECO:0000269|PubMed:23785305}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Ribosome biogenesis in eukaryotes - Homo sapiens (human);rRNA processing;Metabolism of RNA;rRNA modification in the nucleus and cytosol;rRNA processing in the nucleus and cytosol (Consensus)

Intolerance Scores

• loftool: 0.645
• rvis_EVS: 0.1
• rvis_percentile_EVS: 60.76

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.528
• ghis: 0.574

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.877

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Bms1
• 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); vision/eye phenotype

Zebrafish Information Network

• Gene name: bms1
• Affected structure: intestine
• Phenotype tag: abnormal
• Phenotype quality: morphology

Gene ontology

• Biological process: maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA);rRNA processing
• Cellular component: nucleus;nucleoplasm;nucleolus;90S preribosome
• Molecular function: RNA binding;GTPase activity;ATP binding;GTP binding;U3 snoRNA binding