ATRAID

all-trans retinoic acid induced differentiation factor

Basic information

Region (hg38): 2:27212041-27217178

Previous symbols: [ "C2orf28" ]

Links

ENSG00000138085 ∙ NCBI:51374 ∙ OMIM:619682 ∙ HGNC:24090 ∙ Uniprot:Q6UW56 ∙ 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 ATRAID gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATRAID 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						0
missense			16	2		18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			6		1	7
Total	0	0	22	2	1

Variants in ATRAID

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

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

Position	Type	Phenotype	Significance	ClinVar
2-27212208-A-G		not specified	Uncertain significance (May 20, 2024)
2-27212246-A-C		not specified	Uncertain significance (Jan 19, 2024)
2-27212295-G-C		not specified	Uncertain significance (Feb 22, 2023)
2-27212298-G-A		not specified	Uncertain significance (Sep 27, 2022)
2-27212325-C-G		not specified	Uncertain significance (May 27, 2022)
2-27212331-C-T		not specified	Uncertain significance (May 27, 2022)
2-27212345-A-T		not specified	Uncertain significance (Feb 15, 2023)
2-27212381-G-T		not specified	Uncertain significance (Feb 06, 2023)
2-27212393-C-T		not specified	Uncertain significance (Jan 30, 2024)
2-27212447-A-G		not specified	Uncertain significance (Apr 07, 2022)
2-27212465-G-A		not specified	Uncertain significance (Feb 16, 2023)
2-27213202-T-C		not specified	Uncertain significance (Oct 14, 2021)
2-27213222-G-C		not specified	Uncertain significance (Nov 30, 2022)
2-27213277-A-G		not specified	Uncertain significance (May 07, 2024)
2-27215499-G-A		not specified	Uncertain significance (Jan 23, 2023)
2-27215520-C-T		not specified	Uncertain significance (May 23, 2023)
2-27215521-G-A		not specified	Likely benign (Jun 28, 2022)
2-27215633-A-G		not specified	Likely benign (Apr 06, 2024)
2-27215648-G-C		not specified	Uncertain significance (Jan 31, 2022)
2-27215699-G-T		not specified	Uncertain significance (Jun 23, 2021)
2-27215724-A-G		not specified	Likely benign (Dec 01, 2023)
2-27215735-A-G		not specified	Uncertain significance (Jul 20, 2021)
2-27215742-C-G		not specified	Uncertain significance (Nov 13, 2023)
2-27216546-T-C		not specified	Uncertain significance (Mar 11, 2024)
2-27216598-A-T		not specified	Uncertain significance (Aug 08, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ATRAID	protein_coding	protein_coding	ENST00000380171	7	5152

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000105	0.826	125712	0	36	125748	0.000143

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.02	197	161	1.23	0.00000825	1797
Missense in Polyphen		59	55.455	1.0639		625
Synonymous	-0.467	68	63.3	1.07	0.00000326	590
Loss of Function	1.25	8	12.8	0.623	6.16e-7	151

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000618	0.000618
Ashkenazi Jewish	0.00	0.00
East Asian	0.000435	0.000435
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000352	0.0000352
Middle Eastern	0.000435	0.000435
South Asian	0.000163	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Promotes osteoblast cell differentiation and terminal mineralization. Plays a role in inducing the cell cycle arrest via inhibiting CCND1 expression in all-trans-retinoic acid (ATRA) signal pathway. {ECO:0000269|PubMed:21723284}.

Recessive Scores

• pRec: 0.0679

Intolerance Scores

• rvis_EVS: 0.53
• rvis_percentile_EVS: 80.73

Haploinsufficiency Scores

• pHI: 0.0560
• hipred: N
• hipred_score: 0.145
• ghis: 0.403

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Atraid
• Phenotype: vision/eye phenotype

Gene ontology

• Biological process: regulation of gene expression;cell differentiation;positive regulation of bone mineralization;negative regulation of osteoblast proliferation;positive regulation of osteoblast differentiation;negative regulation of cellular protein catabolic process
• Cellular component: nuclear envelope;lysosomal membrane;plasma membrane;integral component of membrane;perinuclear region of cytoplasm
• Molecular function: molecular_function;protein binding