ATRNL1

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

Basic information

Region (hg38): 10:115093364-115948999

Links

ENSG00000107518 ∙ NCBI:26033 ∙ OMIM:612869 ∙ HGNC:29063 ∙ Uniprot:Q5VV63 ∙ 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 ATRNL1 gene.

• Inborn genetic diseases (42 variants)
• not provided (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATRNL1 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				2	1	3
missense			42		2	44
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	2	3

Variants in ATRNL1

This is a list of pathogenic ClinVar variants found in the ATRNL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-115093802-G-A		not specified	Uncertain significance (Aug 30, 2021)
10-115093863-A-C		not specified	Uncertain significance (May 10, 2022)
10-115093887-A-G		not specified	Uncertain significance (May 09, 2023)
10-115093991-T-A		not specified	Uncertain significance (Jul 13, 2021)
10-115093998-C-T		not specified	Uncertain significance (Oct 10, 2023)
10-115120264-G-A		not specified	Uncertain significance (Dec 28, 2022)
10-115121772-G-A		not specified	Uncertain significance (Nov 15, 2021)
10-115121790-G-A		not specified	Uncertain significance (Sep 26, 2023)
10-115129435-T-C			Likely benign (Apr 01, 2022)
10-115129466-G-A		not specified	Uncertain significance (Aug 10, 2021)
10-115129485-A-C		not specified	Uncertain significance (May 03, 2023)
10-115129527-G-A		not specified	Uncertain significance (Dec 03, 2021)
10-115160047-T-A		not specified	Uncertain significance (Jun 22, 2023)
10-115160048-T-C		not specified	Uncertain significance (Apr 07, 2022)
10-115160073-A-C		not specified	Uncertain significance (Dec 21, 2023)
10-115160211-T-C		not specified	Uncertain significance (Nov 07, 2022)
10-115165634-G-T		not specified	Uncertain significance (Oct 26, 2021)
10-115171112-A-G			Benign (Feb 12, 2018)
10-115171116-A-G		not specified	Uncertain significance (Jan 26, 2022)
10-115171199-A-G		not specified	Uncertain significance (May 27, 2022)
10-115215728-A-T		not specified	Uncertain significance (Feb 22, 2023)
10-115215745-G-A		not specified	Uncertain significance (Dec 08, 2023)
10-115215756-C-T		not specified	Uncertain significance (Apr 13, 2022)
10-115215832-A-G		not specified	Uncertain significance (Jan 23, 2024)
10-115215862-A-G		not specified	Uncertain significance (Dec 19, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ATRNL1	protein_coding	protein_coding	ENST00000355044	29	855380

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.000848	125720	0	28	125748	0.000111

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.91	566	709	0.798	0.0000341	9035
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000365	0.000363
Ashkenazi Jewish	0.0000994	0.0000992
East Asian	0.000172	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000107	0.000105
Middle Eastern	0.000172	0.000163
South Asian	0.0000328	0.0000327
Other	0.000515	0.000489

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.599
• hipred: N
• hipred_score: 0.462
• ghis: 0.549

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.666

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Atrnl1
• Phenotype: muscle 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); 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)

Gene ontology

• Biological process: G protein-coupled receptor signaling pathway
• Cellular component: integral component of membrane
• Molecular function: carbohydrate binding