ELAC1

elaC ribonuclease Z 1, the group of MBL fold containing DNA/RNA interacting subfamily|Endoribonucleases

Basic information

Region (hg38): 18:50967991-50988121

Links

ENSG00000141642 ∙ NCBI:55520 ∙ OMIM:608079 ∙ HGNC:14197 ∙ Uniprot:Q9H777 ∙ 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 ELAC1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ELAC1 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						0
missense			20			20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	0	0

Variants in ELAC1

This is a list of pathogenic ClinVar variants found in the ELAC1 region.

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

Position	Type	Phenotype	Significance	ClinVar
18-50974459-C-T		not specified	Uncertain significance (Oct 24, 2023)
18-50974484-G-A		not specified	Uncertain significance (Apr 07, 2022)
18-50984156-G-A		not specified	Uncertain significance (Oct 26, 2022)
18-50984185-G-C		not specified	Uncertain significance (Dec 16, 2023)
18-50984236-C-T		not specified	Uncertain significance (May 29, 2024)
18-50984281-G-C		not specified	Uncertain significance (Dec 11, 2023)
18-50984305-C-G		not specified	Uncertain significance (May 20, 2024)
18-50984377-C-G		not specified	Uncertain significance (May 07, 2024)
18-50984411-T-C		not specified	Uncertain significance (Nov 07, 2022)
18-50984428-T-A		not specified	Uncertain significance (Jun 11, 2021)
18-50984473-C-T		not specified	Uncertain significance (Jun 24, 2022)
18-50984476-C-G		not specified	Uncertain significance (Sep 20, 2023)
18-50984522-A-C		not specified	Uncertain significance (Jun 05, 2023)
18-50984525-G-A		not specified	Uncertain significance (Apr 07, 2022)
18-50984530-G-C		not specified	Uncertain significance (Mar 16, 2022)
18-50986710-A-T		not specified	Uncertain significance (Dec 04, 2023)
18-50986718-C-T		not specified	Uncertain significance (Aug 22, 2023)
18-50986799-C-A		not specified	Uncertain significance (Feb 05, 2024)
18-50986816-G-A		not specified	Uncertain significance (Oct 12, 2022)
18-50986838-A-T		not specified	Uncertain significance (Aug 10, 2021)
18-50986847-A-C		not specified	Uncertain significance (Apr 17, 2023)
18-50986870-A-T		not specified	Uncertain significance (Feb 27, 2024)
18-50986906-C-T		not specified	Uncertain significance (Aug 10, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ELAC1	protein_coding	protein_coding	ENST00000269466	3	20131

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.881	0.119	125734	0	12	125746	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.436	177	194	0.912	0.00000981	2370
Missense in Polyphen		54	69.282	0.77942		821
Synonymous	0.814	64	72.8	0.879	0.00000363	740
Loss of Function	2.84	1	11.3	0.0883	5.62e-7	145

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.000164	0.000163
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000353	0.0000352
Middle Eastern	0.000164	0.000163
South Asian	0.000105	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Zinc phosphodiesterase, which displays some tRNA 3'- processing endonuclease activity. Probably involved in tRNA maturation, by removing a 3'-trailer from precursor tRNA.
• Pathway: RNA transport - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.164

Intolerance Scores

• loftool: 0.494
• rvis_EVS: 0.02
• rvis_percentile_EVS: 55.22

Haploinsufficiency Scores

• pHI: 0.152
• hipred: N
• hipred_score: 0.471
• ghis: 0.559

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.258

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Elac1
• Phenotype: normal phenotype

Gene ontology

• Biological process: tRNA 3'-trailer cleavage, endonucleolytic
• Cellular component: nucleus;cytosol
• Molecular function: 3'-tRNA processing endoribonuclease activity;metal ion binding