RBMXL2

protein-coding

RBMX like 2, the group of RNA binding motif containing

Gene summary

This gene belongs to the HNRPG subfamily of ubiquitously expressed heterogeneous nuclear ribonucleoproteins (hnRNPs). The hnRNPs are RNA binding proteins and they complex with heterogeneous nuclear RNA (hnRNA). These proteins are associated with pre-mRNAs in the nucleus and appear to influence pre-mRNA processing and other aspects of mRNA metabolism and transport. While all of the hnRNPs are present in the nucleus, some seem to shuttle between the nucleus and the cytoplasm. The hnRNP proteins have distinct nucleic acid binding properties. The protein encoded by this gene has two RRM domains that bind RNAs. This gene is intronless and is thought to be derived from a processed retroposon. However, unlike many retroposon-derived genes, this gene is not a pseudogene. The encoded protein has similarity to HNRPG and RBMY proteins and it is suggested to replace HNRPG protein function during meiotic prophase or act as a germ cell-specific splicing regulator. It primarily localizes to the nuclei of meiotic spermatocytes. This gene is a candidate for autosomal male infertility. [provided by RefSeq, Jul 2008]

MANE transcript

NM_014469.5

Inheritance

—

ClinVar variants

U:95B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.32

Max pathogenic AF

—

Genomic locus

chr11:7,088,998-7,091,148

External References & Databases

Ensembl (ENSG00000170748)

Transcript & Mutation Effects

hg38 • Region Span ~2.2 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 RBMXL2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 99

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_014469.5. 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						0
missense			95 clinvar	4 clinvar		99
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	95	4	0	99

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 2 of 2 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_014469.5	RefSeq	NP_055284.3	1	MANE Select
ENST00000306904.7	Ensembl	ENSP00000304139.5	1	MANE Select

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Spliceosome - Homo sapiens (human)

Biological Process

mRNA splicing, via spliceosome

Molecular Function

mRNA binding

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000306904
Coding exons: 1
Length: 2215
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.242	253	264	0.958	0.0000209	2386
Missense (PolyPhen)		16	30.477	0.52499		285
Synonymous	-0.344	123	118	1.04	0.00000987	873
Loss of Function	2.23	4	12.5	0.320	9.96e-7	107

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	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.460

Gene Damage Prediction

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