ATRN

attractin, the group of C-type lectin domain containing

Basic information

Region (hg38): 20:3471018-3651118

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 (313 variants)
not_specified (166 variants)
ATRN-related_disorder (29 variants)
Thrombocytopenia (1 variants)
Autism (1 variants)
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. These statistics are base on transcript: NM_000139321.3. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous			4 clinvar	97 clinvar	6 clinvar	107
missense			270 clinvar	8 clinvar	9 clinvar	287
nonsense			2 clinvar			2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			10 clinvar		2 clinvar	12
Total	0	0	286	105	17

Loading clinvar variants...

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
		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

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

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