RALY

RALY heterogeneous nuclear ribonucleoprotein, the group of MicroRNA protein coding host genes|RNA binding motif containing

Basic information

Region (hg38): 20:33993645-34108308

Links

ENSG00000125970 ∙ NCBI:22913 ∙ OMIM:614663 ∙ HGNC:15921 ∙ Uniprot:Q9UKM9 ∙ 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 RALY gene.

• Inborn genetic diseases (5 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RALY 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					1	1
missense			5		1	6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	5	0	2

Variants in RALY

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

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

Position	Type	Phenotype	Significance	ClinVar
20-34072129-A-G		not specified	Uncertain significance (Jul 06, 2021)
20-34072265-A-G		not specified	Uncertain significance (Oct 30, 2023)
20-34075911-G-A			Benign (May 16, 2018)
20-34075966-G-A		not specified	Uncertain significance (Apr 28, 2022)
20-34076732-C-T		not specified	Uncertain significance (Nov 21, 2023)
20-34076777-G-A		not specified	Uncertain significance (Jun 18, 2021)
20-34077034-A-G		not specified	Uncertain significance (Jun 11, 2021)
20-34077074-T-C			Benign (May 16, 2018)
20-34077108-G-A		not specified	Uncertain significance (Jun 09, 2022)
20-34077189-C-T		not specified	Uncertain significance (Nov 21, 2023)
20-34089745-A-G			Likely benign (Jul 20, 2018)
20-34089747-G-A		not specified	Uncertain significance (Apr 07, 2022)
20-34096758-C-G		not specified	Uncertain significance (Aug 02, 2021)
20-34097422-G-A			Benign (Mar 29, 2018)
20-34105429-C-G			Likely benign (Aug 15, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RALY	protein_coding	protein_coding	ENST00000246194	7	114663

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.138	0.858	125742	0	6	125748	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.36	145	199	0.729	0.0000131	1951
Missense in Polyphen		33	70.783	0.46621		720
Synonymous	0.289	80	83.4	0.960	0.00000590	649
Loss of Function	2.52	4	14.3	0.280	8.39e-7	161

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000447	0.0000439
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: RNA-binding protein that acts as a transcriptional cofactor for cholesterol biosynthetic genes in the liver. Binds the lipid-responsive non-coding RNA LeXis and is required for LeXis-mediated effect on cholesterogenesis (By similarity). May be a heterogeneous nuclear ribonucleoprotein (hnRNP) (PubMed:9376072). {ECO:0000250|UniProtKB:Q64012, ECO:0000269|PubMed:9376072}.

Recessive Scores

• pRec: 0.135

Intolerance Scores

• loftool: 0.261
• rvis_EVS: -0.09
• rvis_percentile_EVS: 46.74

Haploinsufficiency Scores

• pHI: 0.180
• hipred: Y
• hipred_score: 0.825
• ghis: 0.463

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.992

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Raly
• Phenotype: normal phenotype

Gene ontology

• Biological process: mRNA splicing, via spliceosome;cholesterol homeostasis;regulation of nucleic acid-templated transcription
• Cellular component: nucleus;catalytic step 2 spliceosome
• Molecular function: transcription coregulator activity;RNA binding;protein binding