ATRN

attractin, the group of C-type lectin domain containing

Basic information

Region (hg38): 20:3471017-3651118

Links

ENSG00000088812 ∙ NCBI:8455 ∙ OMIM:603130 ∙ HGNC:885 ∙ Uniprot:O75882 ∙ 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 ATRN gene.

• not provided (221 variants)
• Inborn genetic diseases (48 variants)
• ATRN-related condition (3 variants)
• Autism;Thrombocytopenia;Global developmental delay (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATRN 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	61	11	73
missense			124	5	11	140
nonsense			1			1
start loss						0
frameshift						0
inframe indel			4			4
splice donor/acceptor (+/-2bp)			1		2	3
splice region			4	9	2	15
non coding				19	3	22
Total	0	0	131	85	27

Variants in ATRN

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

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

Position	Type	Phenotype	Significance	ClinVar
20-3471064-T-G		ATRN-related disorder	Likely benign (Jun 27, 2019)
20-3471121-C-T		not specified	Uncertain significance (Aug 28, 2023)
20-3471142-TGAG-T			Uncertain significance (Mar 01, 2022)
20-3471152-G-A			Likely benign (Mar 20, 2023)
20-3471160-C-T			Uncertain significance (Dec 09, 2023)
20-3471161-G-C			Likely benign (Jul 12, 2022)
20-3471167-A-C			Benign (Nov 06, 2023)
20-3471170-G-A		ATRN-related disorder	Likely benign (Dec 22, 2023)
20-3471175-C-G		not specified	Uncertain significance (Jul 20, 2021)
20-3471175-C-T			Uncertain significance (Mar 01, 2022)
20-3471188-C-T			Likely benign (Jul 06, 2022)
20-3471189-G-T		not specified	Uncertain significance (Mar 12, 2024)
20-3471200-G-C			Uncertain significance (Jul 07, 2023)
20-3471204-T-C		not specified	Uncertain significance (Apr 10, 2023)
20-3471242-C-G			Likely benign (Jan 12, 2024)
20-3471244-G-A		not specified	Uncertain significance (Jan 23, 2023)
20-3471252-C-T		not specified	Uncertain significance (May 31, 2023)
20-3471261-C-T			Benign (Jan 26, 2024)
20-3471283-C-A			Uncertain significance (Jul 18, 2022)
20-3471284-A-C		ATRN-related disorder	Likely benign (Feb 21, 2019)
20-3471293-G-A			Likely benign (Aug 16, 2022)
20-3471303-T-C			Benign (Dec 02, 2021)
20-3471311-C-G			Likely benign (Nov 08, 2022)
20-3471313-C-G			Uncertain significance (Feb 02, 2023)
20-3471319-C-CGCT			Uncertain significance (Jan 24, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ATRN	protein_coding	protein_coding	ENST00000262919	29	180083

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	3.82e-7	125383	5	360	125748	0.00145

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.69	552	760	0.726	0.0000397	9397
Missense in Polyphen		118	250.39	0.47126		3028
Synonymous	1.01	256	277	0.923	0.0000152	2658
Loss of Function	7.40	9	80.7	0.111	0.00000450	911

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000245	0.000241
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.00159	0.00158
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000168	0.000158
Middle Eastern	0.00159	0.00158
South Asian	0.0101	0.0100
Other	0.000490	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in the initial immune cell clustering during inflammatory response and may regulate chemotactic activity of chemokines. May play a role in melanocortin signaling pathways that regulate energy homeostasis and hair color. Low-affinity receptor for agouti (By similarity). Has a critical role in normal myelination in the central nervous system (By similarity). {ECO:0000250, ECO:0000269|PubMed:9736737}.

Recessive Scores

• pRec: 0.174

Intolerance Scores

• loftool: 0.303
• rvis_EVS: 0.12
• rvis_percentile_EVS: 62.19

Haploinsufficiency Scores

• pHI: 0.278
• hipred: Y
• hipred_score: 0.728
• ghis: 0.515

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.376

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Atrn
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); pigmentation phenotype; reproductive system phenotype; 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); 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); 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); endocrine/exocrine gland phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; muscle phenotype

Gene ontology

• Biological process: inflammatory response;response to oxidative stress;cerebellum development;regulation of multicellular organism growth;myelination;pigmentation
• Cellular component: extracellular space;cytoplasm;plasma membrane;integral component of plasma membrane;extracellular exosome
• Molecular function: carbohydrate binding;signaling receptor activity