ELAC1

protein-coding

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

Gene summary

Enables tRNA-specific ribonuclease activity. Involved in rescue of stalled cytosolic ribosome and tRNA 3'-end processing. Located in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_018696.3

Inheritance

—

ClinVar variants

U:49B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.09

Max pathogenic AF

—

Genomic locus

chr18:50,967,991-50,988,121

External References & Databases

Ensembl (ENSG00000141642)

Transcript & Mutation Effects

hg38 • Region Span ~20.1 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 ELAC1 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 46

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_018696.3. 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			48 clinvar	1 clinvar		49
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	49	1	0	50

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 28 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_018696.3	RefSeq	NP_061166.1	3	MANE Select
ENST00000269466.8	Ensembl	ENSP00000269466.3	3	MANE Select
ENST00000588577.5	Ensembl	ENSP00000467389.1	3	Standard
ENST00000588577.6	Ensembl	ENSP00000467389.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

RNA transport - Homo sapiens (human)

Biological Process

tRNA 3'-trailer cleavage, endonucleolytic

Molecular Function

3'-tRNA processing endoribonuclease activity
metal ion binding

Cellular Component

nucleus
cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000269466
Coding exons: 3
Length: 20131
Individuals with no LoFs: 125734
Homozygous LoFs: 0
Heterozygous LoFs: 12
Defined: 125746
p: 0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.436	177	194	0.912	0.00000981	2370
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00016	0.00016	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.000035	0.000035	rare
South Asian	0.00010	0.000098	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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.;

Recessive Scores

pRec: 0.164

Intolerance Scores

LoFtool: 0.494
RVIS EVS: 0.02
RVIS percentile EVS: 55.22

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.258

Gene Damage Prediction

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