ATRNL1

protein-coding

attractin like 1, the group of C-type lectin domain containing

Gene summary

Predicted to enable Notch binding activity. Predicted to act upstream of or within G protein-coupled receptor signaling pathway. Predicted to be located in membrane. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_207303.4

Inheritance

—

ClinVar variants

U:186B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.17

Max pathogenic AF

—

Genomic locus

chr10:115,093,365-115,948,999

External References & Databases

Ensembl (ENSG00000107518)

Transcript & Mutation Effects

hg38 • Region Span ~855.6 kb

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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 ATRNL1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 172

not providedTotal: 7

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_207303.4. 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	2 clinvar		3
missense			174 clinvar	1 clinvar	1 clinvar	176
nonsense			1 clinvar			1
start loss						0
frameshift			2 clinvar			2
splice donor/acceptor (+/-2bp)			8 clinvar			8
Total	0	0	186	3	1	190

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 28 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_207303.4	RefSeq	NP_997186.1	29	MANE Select
ENST00000355044.8	Ensembl	ENSP00000347152.3	29	MANE Select
NM_001276282.4	RefSeq	NP_001263211.1	8	Standard
ENST00000526373.1	Ensembl	ENSP00000434118.1	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

G protein-coupled receptor signaling pathway

Molecular Function

carbohydrate binding

Cellular Component

integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000355044
Coding exons: 29
Length: 855380
Individuals with no LoFs: 125720
Homozygous LoFs: 0
Heterozygous LoFs: 28
Defined: 125748
p: 0.000111

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.91	566	709	0.798	0.0000341	9035
Missense (PolyPhen)		170	279.76	0.60766		3531
Synonymous	0.435	235	244	0.965	0.0000121	2513
Loss of Function	6.81	13	77.8	0.167	0.00000386	955

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00025	0.00025	rare
Latino/Admixed American	0.00012	0.00012	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.00017	0.00016	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00011	0.00011	rare
South Asian	0.000033	0.000033	rare
Other	0.00051	0.00049	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May play a role in melanocortin signaling pathways that regulate energy homeostasis. {ECO:0000250}.;

Recessive Scores

pRec: 0.108

Intolerance Scores

LoFtool: 0.699
RVIS EVS: -1.59
RVIS percentile EVS: 3.07

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.666

Gene Damage Prediction

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