RASEF

protein-coding

RAS and EF-hand domain containing, the group of RAB, member RAS oncogene GTPases|EF-hand domain containing

Gene summary

This gene is a member of the Rab family of GTPases that are involved in regulation of membrane traffic. The encoded protein contains an N-terminal EF-hand domain, a coiled-coil motif and a C-terminal Rab domain. A potential role as tumor suppressor has been indicated for this gene. [provided by RefSeq, Nov 2012]

Previous symbols:

RAB45

MANE transcript

NM_152573.4

Inheritance

—

ClinVar variants

U:124B:6

Top phenotype

RASEF-related disorder

gnomAD constraint

pLI —, LoF o/e 0.51

Max pathogenic AF

—

Genomic locus

chr9:82,979,590-83,063,177

External References & Databases

Ensembl (ENSG00000165105)

Transcript & Mutation Effects

hg38 • Region Span ~83.6 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 RASEF variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 114

not providedTotal: 1

RASEF-related disorderTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_152573.4. 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			4 clinvar	1 clinvar		5
missense			112 clinvar	5 clinvar		117
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			8 clinvar			8
Total	0	0	124	6	0	130

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 20 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_152573.4	RefSeq	NP_689786.2	17	MANE Select
ENST00000376447.4	Ensembl	ENSP00000365630.3	17	MANE Select
ENST00000340717.4	Ensembl	ENSP00000345651.4	2	Standard
ENST00000340717.5	Ensembl	ENSP00000345651.4	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

protein homooligomerization

Molecular Function

GTPase activity
calcium ion binding
GTP binding
GDP binding
identical protein binding

Cellular Component

cytosol
perinuclear region of cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000376447
Coding exons: 17
Length: 83593
Individuals with no LoFs: 125643
Homozygous LoFs: 0
Heterozygous LoFs: 105
Defined: 125748
p: 0.000418

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.0241	400	401	0.997	0.0000202	4832
Missense (PolyPhen)		141	144.06	0.97873		1917
Synonymous	1.74	123	150	0.819	0.00000754	1386
Loss of Function	2.88	21	40.9	0.514	0.00000232	461

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.00041	0.00040	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0.0011	0.0011	notable
European (Non-Finnish)	0.00051	0.00051	rare
South Asian	0.00011	0.000098	rare
Other	0.00049	0.00049	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Binds predominantly GDP, and also GTP. {ECO:0000269|PubMed:17448446}.;

Intolerance Scores

LoFtool: 0.571
RVIS EVS: 0.42
RVIS percentile EVS: 77.23

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.443

Gene Damage Prediction

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