ATRN

protein-coding

attractin, the group of C-type lectin domain containing

Gene summary

This gene encodes both membrane-bound and secreted protein isoforms. A membrane-bound isoform exhibits sequence similarity with the mouse mahogany protein, a receptor involved in controlling obesity. A secreted isoform is involved in the initial immune cell clustering during inflammatory responses that may regulate the chemotactic activity of chemokines. [provided by RefSeq, Apr 2016]

MANE transcript

NM_139321.3

Inheritance

—

ClinVar variants

U:291B:123

Top phenotype

ATRN-related disorder

gnomAD constraint

pLI —, LoF o/e 0.11

Max pathogenic AF

—

Genomic locus

chr20:3,471,018-3,651,118

External References & Databases

Ensembl (ENSG00000088812)

Transcript & Mutation Effects

hg38 • Region Span ~180.1 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 ATRN variants in ClinVar

6 Conditions Cataloged

not providedTotal: 317

not specifiedTotal: 170

ATRN-related disorderTotal: 29

ThrombocytopeniaTotal: 1

AutismTotal: 1

Global developmental delayTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_139321.3. 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			4 clinvar	99 clinvar	6 clinvar	109
missense			274 clinvar	8 clinvar	9 clinvar	291
nonsense			2 clinvar			2
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			10 clinvar		1 clinvar	11
Total	0	0	291	107	16	414

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 15 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_139321.3	RefSeq	NP_647537.1	29	MANE Select
ENST00000262919.10	Ensembl	ENSP00000262919.5	29	MANE Select
NM_001207047.3	RefSeq	NP_001193976.1	25	Standard
NM_001323332.2	RefSeq	NP_001310261.1	26	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

inflammatory response
response to oxidative stress
cerebellum development
regulation of multicellular organism growth
myelination

Molecular Function

carbohydrate binding
signaling receptor activity

Cellular Component

extracellular space
cytoplasm
plasma membrane
integral component of plasma membrane
extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000262919
Coding exons: 29
Length: 180083
Individuals with no LoFs: 125383
Homozygous LoFs: 5
Heterozygous LoFs: 360
Defined: 125748
p: 0.00145

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.69	552	760	0.726	0.0000397	9397
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000065	0.000062	rare
Latino/Admixed American	0.00018	0.00017	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.0016	0.0016	notable
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00017	0.00016	rare
South Asian	0.010	0.010	notable
Other	0.00049	0.00049	rare

dbNSFP Gene Annotations

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 (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.376

Gene Damage Prediction

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