ATMIN

protein-coding

ATM interactor, the group of Zinc fingers C2H2-type

Gene summary

Enables dynein complex binding activity. Involved in positive regulation of DNA-templated transcription. Located in nuclear body. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_015251.3

Inheritance

—

ClinVar variants

U:145B:9

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.47

Max pathogenic AF

—

Genomic locus

chr16:81,035,842-81,047,350

External References & Databases

Ensembl (ENSG00000166454)

Transcript & Mutation Effects

hg38 • Region Span ~11.5 kb

Loading mutation effect viewer...

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 ATMIN variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 145

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_015251.3. 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			1 clinvar	1 clinvar		2
missense			141 clinvar	8 clinvar		149
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	145	9	0	154

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 19 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_015251.3	RefSeq	NP_056066.2	4	MANE Select
ENST00000299575.5	Ensembl	ENSP00000299575.3	4	MANE Select
NM_001300728.2	RefSeq	NP_001287657.1	2	Standard
ENST00000564241.5	Ensembl	ENSP00000463478.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

ATM Signaling Network in Development and Disease

Biological Process

cellular response to DNA damage stimulus
motile cilium assembly
positive regulation of transcription, DNA-templated
positive regulation of non-motile cilium assembly

Molecular Function

protein binding
transcription regulatory region DNA binding
metal ion binding
dynein complex binding

Cellular Component

nuclear body

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000299575
Coding exons: 4
Length: 11512
Individuals with no LoFs: 125702
Homozygous LoFs: 0
Heterozygous LoFs: 45
Defined: 125747
p: 0.000179

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.735	451	409	1.10	0.0000205	5380
Missense (PolyPhen)		92	98.084	0.93797		1361
Synonymous	-2.16	199	164	1.22	0.00000968	1679
Loss of Function	2.40	11	23.6	0.466	0.00000109	309

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00025	0.00025	rare
Latino/Admixed American	0.00015	0.00014	rare
Ashkenazi Jewish	0.00020	0.00020	rare
East Asian	0.00011	0.00011	rare
Finnish	0.000092	0.000092	rare
European (Non-Finnish)	0.000097	0.000097	rare
South Asian	0.00062	0.00062	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Transcription factor. Plays a crucial role in cell survival and RAD51 foci formation in response to methylating DNA damage. Involved in regulating the activity of ATM in the absence of DNA damage. May play a role in stabilizing ATM. Binds to the DYNLL1 promoter and activates its transcription. {ECO:0000269|PubMed:15933716, ECO:0000269|PubMed:17525732, ECO:0000269|PubMed:22167198}.;

Recessive Scores

pRec: 0.110

Intolerance Scores

LoFtool: 0.652
RVIS EVS: -0.88
RVIS percentile EVS: 10.5

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.252

Gene Damage Prediction

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