RALY

protein-coding

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

Gene summary

This gene encodes a member of the heterogeneous nuclear ribonucleoprotein (hnRNP) gene family. This protein may play a role in pre-mRNA splicing and in embryonic development. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Sep 2011]

MANE transcript

NM_016732.3

Inheritance

—

ClinVar variants

U:50B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.28

Max pathogenic AF

—

Genomic locus

chr20:33,993,646-34,108,308

External References & Databases

Ensembl (ENSG00000125970)

Transcript & Mutation Effects

hg38 • Region Span ~114.7 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to RALY variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 36

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_016732.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			3 clinvar		1 clinvar	4
missense			36 clinvar	2 clinvar	1 clinvar	39
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			10 clinvar			10
Total	0	0	50	2	2	54

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 134 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_016732.3	RefSeq	NP_057951.1	7	MANE Select
ENST00000246194.8	Ensembl	ENSP00000246194.3	7	MANE Select
NM_007367.4	RefSeq	NP_031393.2	6	Standard
ENST00000333552.9	Ensembl	ENSP00000327522.5	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

mRNA splicing, via spliceosome
cholesterol homeostasis
regulation of nucleic acid-templated transcription

Molecular Function

transcription coregulator activity
RNA binding
protein binding

Cellular Component

nucleus
catalytic step 2 spliceosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000246194
Coding exons: 7
Length: 114663
Individuals with no LoFs: 125742
Homozygous LoFs: 0
Heterozygous LoFs: 6
Defined: 125748
p: 0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.36	145	199	0.729	0.0000131	1951
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000045	0.000044	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.992

Gene Damage Prediction

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