RBMY1A1

RNA binding motif protein Y-linked family 1 member A1, the group of RNA binding motif containing

Basic information

Region (hg38): Y:21534879-21549326

Previous symbols: [ "RBM1", "RBM2" ]

Links

ENSG00000234414 ∙ NCBI:5940 ∙ OMIM:400006 ∙ HGNC:9912 ∙ Uniprot:P0DJD3 ∙ 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 RBMY1A1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RBMY1A1 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			1			1
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	1	0	0

Variants in RBMY1A1

This is a list of pathogenic ClinVar variants found in the RBMY1A1 region.

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

Position	Type	Phenotype	Significance	ClinVar
Y-21548157-G-T			Uncertain significance (Jan 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RBMY1A1	protein_coding	protein_coding	ENST00000382707	11	37955

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.290	0.501	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.336	0	0.896	0.00	1.37e-7	3220
Missense in Polyphen		0	0.054848	0		701
Synonymous	0.429	0	0.298	0.00	4.07e-8	974
Loss of Function	0.284	0	0.0939	0.00	1.26e-8	286

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: RNA-binding protein involved in pre-mRNA splicing. Required for sperm development. Acts additively with TRA2B to promote exon 7 inclusion of the survival motor neuron SMN. Binds non-specifically to mRNAs. {ECO:0000269|PubMed:12165565, ECO:0000269|PubMed:8269511}.

Haploinsufficiency Scores

• ghis: 0.394

Essentials

• essential_gene_CRISPR: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0382

Gene ontology

• Biological process: regulation of alternative mRNA splicing, via spliceosome;mRNA cis splicing, via spliceosome
• Cellular component: nucleus;nuclear speck
• Molecular function: RNA binding;mRNA binding;protein binding