RBM28

RNA binding motif protein 28, the group of RNA binding motif containing

Basic information

Region (hg38): 7:128297685-128343908

Links

ENSG00000106344 ∙ NCBI:55131 ∙ OMIM:612074 ∙ HGNC:21863 ∙ Uniprot:Q9NW13 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• ANE syndrome (Limited), mode of inheritance: AR
• ANE syndrome (Supportive), mode of inheritance: AR
• ANE syndrome (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Alopecia, neurologic defects, and endocrinopathy syndrome	AR	Endocrine	Features may include progressive endocrine abnormalities primarily related to progressive anterior pituitary hormone deficiency, including central adrenal insufficiency, as well as other endocrine deficiencies, and surveillance in order to allow appropriate hormonal replacement therapy may be beneficial	Dermatologic; Endocrine; Musculoskeletal; Neurologic	18439547; 20231366

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RBM28 gene.

• not_specified (85 variants)
• not_provided (32 variants)
• RBM28-related_disorder (8 variants)
• ANE_syndrome (8 variants)
• Microcephaly (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RBM28 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000018077.3. 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	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			1	14	3	18
missense	1	1	80	12	2	96
nonsense			1			1
start loss						0
frameshift	1	1	2			4
splice donor/acceptor (+/-2bp)	1					1
Total	3	2	84	26	5

Highest pathogenic variant AF is 0.00000743507

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RBM28	protein_coding	protein_coding	ENST00000223073	19	46225

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.23e-12	0.990	125644	0	104	125748	0.000414

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.179	388	398	0.975	0.0000223	5010
Missense in Polyphen		175	178.82	0.97865		2181
Synonymous	0.768	139	151	0.921	0.00000872	1386
Loss of Function	2.52	25	42.8	0.584	0.00000236	532

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000684	0.000684
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.000277	0.000277
European (Non-Finnish)	0.000449	0.000448
Middle Eastern	0.000163	0.000163
South Asian	0.000784	0.000784
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Nucleolar component of the spliceosomal ribonucleoprotein complexes. {ECO:0000269|PubMed:17081119}.
• Pathway: Ribosome biogenesis in eukaryotes - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.0962

Intolerance Scores

• loftool: 0.965
• rvis_EVS: 1
• rvis_percentile_EVS: 90.77

Haploinsufficiency Scores

• pHI: 0.702
• hipred: Y
• hipred_score: 0.692
• ghis: 0.433

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.936

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rbm28

Gene ontology

• Biological process: mRNA processing;RNA splicing
• Cellular component: nucleus;spliceosomal complex;nucleolus;ribonucleoprotein complex
• Molecular function: RNA binding