YJEFN3

YjeF N-terminal domain containing 3

Basic information

Region (hg38): 19:19528861-19537581

Links

ENSG00000250067 ∙ NCBI:374887 ∙ OMIM:618607 ∙ HGNC:24785 ∙ Uniprot:A6XGL0 ∙ 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 YJEFN3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the YJEFN3 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			29	1		30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	29	1	0

Variants in YJEFN3

This is a list of pathogenic ClinVar variants found in the YJEFN3 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-19528957-C-G		not specified	Uncertain significance (Jan 09, 2024)
19-19528967-C-T		not specified	Uncertain significance (May 30, 2024)
19-19528977-G-T		not specified	Uncertain significance (Oct 10, 2023)
19-19528979-G-T		not specified	Uncertain significance (Oct 10, 2023)
19-19529383-C-T		not specified	Uncertain significance (Aug 28, 2023)
19-19529384-C-T		not specified	Uncertain significance (Jan 07, 2025)
19-19529392-G-A		not specified	Uncertain significance (Oct 21, 2021)
19-19529413-A-G		not specified	Uncertain significance (Feb 19, 2025)
19-19529434-C-T		not specified	Uncertain significance (Feb 07, 2023)
19-19529456-C-T		not specified	Uncertain significance (Feb 23, 2023)
19-19529510-A-G		not specified	Uncertain significance (Mar 02, 2023)
19-19532634-C-T		not specified	Uncertain significance (Jan 26, 2022)
19-19532658-G-T		not specified	Uncertain significance (Nov 07, 2024)
19-19532679-G-A		not specified	Uncertain significance (Oct 12, 2024)
19-19532711-G-C		not specified	Uncertain significance (Nov 04, 2023)
19-19532716-T-A		not specified	Uncertain significance (Aug 28, 2024)
19-19535041-C-T		not specified	Uncertain significance (Oct 29, 2021)
19-19535082-G-A		not specified	Uncertain significance (Feb 08, 2025)
19-19535103-G-A		not specified	Uncertain significance (Dec 03, 2024)
19-19535356-T-G		not specified	Uncertain significance (Oct 12, 2022)
19-19535367-C-T		not specified	Uncertain significance (May 09, 2022)
19-19535389-G-A		not specified	Uncertain significance (Jul 09, 2021)
19-19535408-C-G		not specified	Uncertain significance (Nov 18, 2022)
19-19535409-G-A		not specified	Uncertain significance (Jun 06, 2023)
19-19535547-G-A		not specified	Uncertain significance (Jul 09, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
YJEFN3	protein_coding	protein_coding	ENST00000514277	7	21355

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000127	0.627	124517	0	5	124522	0.0000201

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.118	200	195	1.02	0.0000137	1848
Missense in Polyphen		67	66.148	1.0129		692
Synonymous	-0.00170	96	96.0	1.00	0.00000728	649
Loss of Function	0.881	9	12.3	0.729	5.28e-7	141

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000128	0.000127
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000573	0.0000556
Finnish	0.00	0.00
European (Non-Finnish)	0.00000891	0.00000886
Middle Eastern	0.0000573	0.0000556
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in spermiogenesis and oogenesis. {ECO:0000269|PubMed:17533573}.

Intolerance Scores

• rvis_EVS: -0.25
• rvis_percentile_EVS: 35.99

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.123
• ghis: 0.516

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Yjefn3

Zebrafish Information Network

• Gene name: yjefn3
• Affected structure: endothelial tip cell
• Phenotype tag: abnormal
• Phenotype quality: disrupted

Gene ontology

• Cellular component: mitochondrion
• Molecular function: NADHX epimerase activity;NADPHX epimerase activity