ASTE1

protein-coding

asteroid homolog 1

Gene summary

Enables 3' overhang single-stranded DNA endonuclease activity. Involved in double-strand break repair via homologous recombination and double-strand break repair via nonhomologous end joining. Implicated in Lynch syndrome and mismatch repair cancer syndrome. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_014065.4

Inheritance

ClinVar variants

U:100B:8

Top phenotype

ASTE1-related disorder

gnomAD constraint

pLI —, LoF o/e 0.76

Max pathogenic AF

—

Genomic locus

chr3:131,013,875-131,027,649

External References & Databases

Ensembl (ENSG00000034533)

Transcript & Mutation Effects

hg38 • Region Span ~13.8 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

palmar fibromatosisLIMITED

Inheritance Pattern: AD

Disease ID:MONDO:0006345

Submitter: PanelApp Australia

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ASTE1 variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 101

not providedTotal: 1

ASTE1-related disorderTotal: 1

Inborn genetic diseasesTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_014065.4. 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			1 clinvar	1 clinvar		2
missense			96 clinvar	6 clinvar		102
nonsense			2 clinvar	1 clinvar		3
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	100	8	0	108

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 42 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_014065.4	RefSeq	NP_054784.2	4	MANE Select
ENST00000264992.8	Ensembl	ENSP00000264992.3	4	MANE Select
NM_001288950.2	RefSeq	NP_001275879.1	5	Standard
ENST00000504725.1	Ensembl	ENSP00000422851.1	1	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

DNA repair
nucleic acid phosphodiester bond hydrolysis

Molecular Function

nuclease activity
protein binding

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000264992
Coding exons: 4
Length: 13775
Individuals with no LoFs: 125658
Homozygous LoFs: 0
Heterozygous LoFs: 90
Defined: 125748
p: 0.000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.863	316	362	0.872	0.0000185	4449
Missense (PolyPhen)		100	125.3	0.79807		1559
Synonymous	-0.0471	140	139	1.01	0.00000674	1332
Loss of Function	1.06	17	22.4	0.759	0.00000125	262

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.00055	0.00055	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.00022	0.00022	rare
Finnish	0.00024	0.00023	rare
European (Non-Finnish)	0.00045	0.00044	rare
South Asian	0.00027	0.00026	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Possible role in EGF receptor signaling. {ECO:0000250}.;

Recessive Scores

pRec: 0.0834

Intolerance Scores

LoFtool: 0.289
RVIS EVS: 0.0000761
RVIS percentile EVS: 53.98

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.666

Gene Damage Prediction

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