ELAPOR1

endosome-lysosome associated apoptosis and autophagy regulator 1

Basic information

Region (hg38): 1:109113678-109206781

Previous symbols: [ "KIAA1324" ]

Links

ENSG00000116299 ∙ NCBI:57535 ∙ OMIM:611298 ∙ HGNC:29618 ∙ Uniprot:Q6UXG2 ∙ 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 ELAPOR1 gene.

• Inborn genetic diseases (14 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ELAPOR1 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					2	2
missense			14			14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	0	2

Variants in ELAPOR1

This is a list of pathogenic ClinVar variants found in the ELAPOR1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-109114191-A-C		not specified	Uncertain significance (Jun 21, 2021)
1-109114244-C-G		not specified	Uncertain significance (Apr 11, 2023)
1-109114245-G-T		not specified	Uncertain significance (Sep 06, 2022)
1-109114248-T-A		not specified	Uncertain significance (Jan 26, 2022)
1-109114253-C-T		not specified	Uncertain significance (Jul 27, 2022)
1-109114293-A-G		not specified	Uncertain significance (Jun 21, 2021)
1-109161925-A-G		not specified	Uncertain significance (Oct 26, 2021)
1-109161930-A-G		not specified	Uncertain significance (Jul 05, 2023)
1-109161958-C-G		not specified	Uncertain significance (Jan 23, 2024)
1-109161983-C-G		not specified	Uncertain significance (Jan 29, 2024)
1-109164499-C-A		not specified	Uncertain significance (Dec 19, 2023)
1-109164499-C-G		not specified	Uncertain significance (Dec 26, 2023)
1-109164555-T-C		not specified	Uncertain significance (Dec 11, 2023)
1-109164567-C-T		not specified	Uncertain significance (Feb 06, 2024)
1-109164574-C-G		not specified	Uncertain significance (Sep 29, 2022)
1-109164592-G-A		not specified	Uncertain significance (Mar 21, 2022)
1-109164658-A-T		not specified	Uncertain significance (Feb 26, 2024)
1-109164678-G-A		not specified	Uncertain significance (Jan 03, 2022)
1-109171871-A-G		not specified	Uncertain significance (Feb 14, 2023)
1-109171937-C-T		not specified	Uncertain significance (May 31, 2023)
1-109171994-G-A		not specified	Uncertain significance (May 05, 2023)
1-109173478-A-T		not specified	Uncertain significance (Jan 10, 2023)
1-109173487-G-A		not specified	Uncertain significance (Jul 14, 2022)
1-109173729-A-T		not specified	Uncertain significance (Oct 20, 2023)
1-109173775-C-G		not specified	Uncertain significance (Dec 06, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ELAPOR1	protein_coding	protein_coding	ENST00000369939	22	93101

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.03e-13	1.00	125651	1	96	125748	0.000386

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.12	499	575	0.868	0.0000311	6592
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00104	0.00104
Ashkenazi Jewish	0.00	0.00
East Asian	0.000770	0.000761
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000373	0.000352
Middle Eastern	0.000770	0.000761
South Asian	0.000524	0.000490
Other	0.00	0.00

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.189
• hipred: Y
• hipred_score: 0.554
• ghis: 0.437

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.247

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: 5330417C22Rik
• Phenotype: vision/eye phenotype; immune system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); reproductive system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); hematopoietic system phenotype; cellular phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: autophagosome assembly;cellular response to starvation;positive regulation of vacuole organization;positive regulation of autophagosome assembly
• Cellular component: lysosome;lysosomal membrane;late endosome;trans-Golgi network;plasma membrane;integral component of plasma membrane;late endosome membrane;extracellular exosome
• Molecular function: RNA binding