ATMIN

ATM interactor, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 16:81035841-81047350

Links

ENSG00000166454 ∙ NCBI:23300 ∙ OMIM:614693 ∙ HGNC:29034 ∙ Uniprot:O43313 ∙ 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 ATMIN gene.

• Inborn genetic diseases (48 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATMIN 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				1		1
missense			42	7		49
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	42	8	0

Variants in ATMIN

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

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

Position	Type	Phenotype	Significance	ClinVar
16-81035878-C-G		not specified	Uncertain significance (Feb 17, 2022)
16-81035896-C-T		not specified	Uncertain significance (Oct 27, 2022)
16-81035899-C-A		not specified	Uncertain significance (Feb 10, 2023)
16-81035917-C-T		not specified	Uncertain significance (Feb 22, 2023)
16-81035926-C-G		not specified	Uncertain significance (Aug 16, 2022)
16-81035938-C-T		not specified	Uncertain significance (Oct 26, 2022)
16-81035941-C-T		not specified	Likely benign (Dec 05, 2022)
16-81036013-G-A		not specified	Uncertain significance (Sep 30, 2021)
16-81036066-G-A		not specified	Likely benign (Aug 16, 2021)
16-81036131-C-T			Likely benign (Oct 01, 2022)
16-81036165-C-T		not specified	Uncertain significance (Mar 06, 2023)
16-81041360-G-A		not specified	Uncertain significance (Aug 20, 2023)
16-81041364-A-G		not specified	Uncertain significance (Nov 03, 2023)
16-81041407-T-G		not specified	Uncertain significance (Dec 26, 2023)
16-81042312-A-G		not specified	Uncertain significance (Feb 12, 2024)
16-81042321-G-C		not specified	Uncertain significance (Jan 07, 2022)
16-81042324-A-G		not specified	Uncertain significance (Jun 21, 2023)
16-81042393-G-A		not specified	Likely benign (Aug 02, 2023)
16-81042401-T-C		not specified	Uncertain significance (Sep 29, 2023)
16-81042461-G-A		not specified	Uncertain significance (Aug 18, 2021)
16-81043163-A-T		not specified	Uncertain significance (Sep 06, 2022)
16-81043220-A-G		not specified	Likely benign (Apr 25, 2022)
16-81043399-G-C		not specified	Uncertain significance (Aug 08, 2023)
16-81043531-C-T		not specified	Uncertain significance (Jan 04, 2024)
16-81043621-A-C		not specified	Uncertain significance (Dec 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ATMIN	protein_coding	protein_coding	ENST00000299575	4	11512

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000503	0.993	125702	0	45	125747	0.000179

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.735	451	409	1.10	0.0000205	5380
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000400	0.000399
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.000109	0.000109
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.0000968	0.0000967
Middle Eastern	0.000109	0.000109
South Asian	0.000621	0.000621
Other	0.00	0.00

dbNSFP

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}.
• Pathway: ATM Signaling Network in Development and Disease (Consensus)

Recessive Scores

• pRec: 0.110

Intolerance Scores

• loftool: 0.652
• rvis_EVS: -0.88
• rvis_percentile_EVS: 10.5

Haploinsufficiency Scores

• pHI: 0.579
• hipred: Y
• hipred_score: 0.608
• ghis: 0.619

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.252

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Atmin
• Phenotype: homeostasis/metabolism phenotype; cellular phenotype; craniofacial phenotype; endocrine/exocrine gland phenotype; growth/size/body region phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); embryo phenotype; skeleton phenotype; renal/urinary system phenotype; immune system phenotype; vision/eye phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); neoplasm; hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); 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); respiratory system phenotype

Gene ontology

• Biological process: cellular response to DNA damage stimulus;motile cilium assembly;positive regulation of transcription, DNA-templated;positive regulation of non-motile cilium assembly
• Cellular component: nuclear body
• Molecular function: protein binding;transcription regulatory region DNA binding;metal ion binding;dynein complex binding