BMS1

BMS1 ribosome biogenesis factor, the group of SSU processome

Basic information

Region (hg38): 10:42782795-42834937

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
aplasia cutis congenita (Strong), 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.

not_specified (167 variants)
not_provided (40 variants)
BMS1-related_disorder (27 variants)
Aplasia_cutis_congenita (4 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. These statistics are base on transcript: NM_000014753.4. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				18 clinvar	8 clinvar	26
missense	1 clinvar		158 clinvar	15 clinvar	11 clinvar	185
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)						0
Total	1	0	159	33	19

Highest pathogenic variant AF is 0.000009937827

Loading clinvar variants...

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

pHI
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