ELAPOR1

protein-coding

endosome-lysosome associated apoptosis and autophagy regulator 1

Gene summary

Expression of this gene is induced by estrogen and the encoded protein has been characterized as a transmembrane protein. The encoded protein has been found in to correlate with survival in certain carcinomas (PMID: 21102415) and may be important for cellular response to stress (PMID: 21072319). Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2012]

Previous symbols:

KIAA1324

MANE transcript

NM_020775.5

Inheritance

—

ClinVar variants

U:164B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.53

Max pathogenic AF

—

Genomic locus

chr1:109,113,679-109,206,781

External References & Databases

Ensembl (ENSG00000116299)

Transcript & Mutation Effects

hg38 • Region Span ~93.1 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 ELAPOR1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 150

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_020775.5. 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			4 clinvar		2 clinvar	6
missense			152 clinvar	2 clinvar		154
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			8 clinvar			8
Total	0	0	164	2	2	168

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 31 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_020775.5	RefSeq	NP_065826.3	22	MANE Select
ENST00000369939.8	Ensembl	ENSP00000358955.3	22	MANE Select
NM_001267048.2	RefSeq	NP_001253977.2	20	Standard
NM_001284352.2	RefSeq	NP_001271281.1	20	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

autophagosome assembly
cellular response to starvation
positive regulation of vacuole organization
positive regulation of autophagosome assembly

Molecular Function

RNA binding

Cellular Component

lysosome
lysosomal membrane
late endosome
trans-Golgi network
plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000369939
Coding exons: 22
Length: 93101
Individuals with no LoFs: 125651
Homozygous LoFs: 1
Heterozygous LoFs: 96
Defined: 125748
p: 0.000386

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.12	499	575	0.868	0.0000311	6592
Missense (PolyPhen)		162	225.8	0.71745		2669
Synonymous	0.271	232	237	0.978	0.0000148	1973
Loss of Function	3.21	29	54.6	0.531	0.00000280	627

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00049	0.00049	rare
Latino/Admixed American	0.00055	0.00055	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00077	0.00076	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00037	0.00035	rare
South Asian	0.00052	0.00049	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May protect cells from cell death by inducing cytosolic vacuolization and upregulating the autophagy pathway. {ECO:0000269|PubMed:21072319}.;

Recessive Scores

pRec: 0.108

Intolerance Scores

LoFtool: 0.926
RVIS EVS: -0.5
RVIS percentile EVS: 21.84

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.247

Gene Damage Prediction

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