YAE1

YAE1 maturation factor of ABCE1

Basic information

Region (hg38): 7:39566384-39610320

Previous symbols: [ "C7orf36", "YAE1D1" ]

Links

ENSG00000241127 ∙ NCBI:57002 ∙ ∙ HGNC:24857 ∙ Uniprot:Q9NRH1 ∙ 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 YAE1 gene.

• Inborn genetic diseases (3 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the YAE1 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			3		1	4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	3	0	1

Variants in YAE1

This is a list of pathogenic ClinVar variants found in the YAE1 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-39566437-G-A		not specified	Uncertain significance (Aug 14, 2023)
7-39566480-A-T		not specified	Uncertain significance (Aug 01, 2022)
7-39570585-C-A		not specified	Uncertain significance (Sep 22, 2023)
7-39572303-A-G		not specified	Uncertain significance (May 10, 2022)
7-39572365-G-A		not specified	Uncertain significance (Nov 09, 2021)
7-39572386-C-A		not specified	Uncertain significance (Nov 21, 2022)
7-39572399-C-T		not specified	Uncertain significance (Jul 14, 2021)
7-39572435-T-C		not specified	Uncertain significance (Nov 02, 2023)
7-39572485-G-A		not specified	Uncertain significance (Sep 29, 2023)
7-39572488-G-A		not specified	Uncertain significance (Jan 23, 2023)
7-39572507-G-C		not specified	Uncertain significance (Feb 03, 2022)
7-39572602-C-T			Benign (May 24, 2018)
7-39572626-T-A		not specified	Uncertain significance (Jul 12, 2022)
7-39572671-T-C		not specified	Uncertain significance (Aug 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
YAE1	protein_coding	protein_coding	ENST00000223273	3	43945

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00150	0.887	125715	0	32	125747	0.000127

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.288	107	116	0.925	0.00000513	1480
Missense in Polyphen		33	34.453	0.95782		437
Synonymous	0.442	41	44.8	0.916	0.00000206	420
Loss of Function	1.38	6	10.9	0.549	6.54e-7	120

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000163	0.000163
Ashkenazi Jewish	0.000209	0.000198
East Asian	0.000114	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000160	0.000149
Middle Eastern	0.000114	0.000109
South Asian	0.000137	0.000131
Other	0.000343	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: The complex LTO1:YAE1 functions as a target specific adapter that probably recruits apo-ABCE1 to the cytosolic iron- sulfur protein assembly (CIA) complex machinery (PubMed:26182403). May be required for biogenesis of the large ribosomal subunit and initiation of translation (PubMed:26182403). {ECO:0000269|PubMed:26182403}.

Recessive Scores

• pRec: 0.0964

Intolerance Scores

• rvis_EVS: 0.28
• rvis_percentile_EVS: 71.27

Haploinsufficiency Scores

• pHI: 0.121
• hipred: N
• hipred_score: 0.145
• ghis: 0.505

Essentials

• essential_gene_gene_trap: E

Mouse Genome Informatics

• Gene name: Yae1d1

Gene ontology

• Biological process: translational initiation;ribosomal large subunit biogenesis;protein maturation by [4Fe-4S] cluster transfer
• Cellular component: nucleus;cytoplasm