EDDM3B

epididymal protein 3B

Basic information

Region (hg38): 14:20768404-20770948

Previous symbols: [ "FAM12B" ]

Links

ENSG00000181552 ∙ NCBI:64184 ∙ OMIM:611582 ∙ HGNC:19223 ∙ Uniprot:P56851 ∙ 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 EDDM3B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EDDM3B 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	1		17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	1	0

Variants in EDDM3B

This is a list of pathogenic ClinVar variants found in the EDDM3B region.

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

Position	Type	Phenotype	Significance	ClinVar
14-20770185-T-C		not specified	Uncertain significance (Aug 28, 2024)
14-20770193-C-A		not specified	Uncertain significance (Dec 02, 2021)
14-20770197-G-T		not specified	Likely benign (Nov 11, 2024)
14-20770229-G-A		not specified	Uncertain significance (Feb 02, 2022)
14-20770235-T-G		not specified	Uncertain significance (Apr 08, 2022)
14-20770239-G-C		not specified	Uncertain significance (Feb 25, 2025)
14-20770249-C-A		not specified	Uncertain significance (Mar 18, 2024)
14-20770292-T-A		not specified	Uncertain significance (Apr 09, 2024)
14-20770310-A-G		not specified	Uncertain significance (Sep 25, 2024)
14-20770334-G-T		not specified	Uncertain significance (May 16, 2023)
14-20770358-T-G		not specified	Uncertain significance (Jun 17, 2024)
14-20770379-G-A		not specified	Uncertain significance (Dec 18, 2023)
14-20770388-T-C		not specified	Uncertain significance (May 15, 2024)
14-20770419-G-T		not specified	Uncertain significance (Oct 28, 2024)
14-20770427-T-C		not specified	Uncertain significance (Oct 12, 2021)
14-20770507-C-A		not specified	Uncertain significance (Sep 16, 2021)
14-20770541-G-A		not specified	Uncertain significance (Nov 20, 2024)
14-20770545-A-G		not specified	Uncertain significance (Jan 07, 2025)
14-20770581-C-G		not specified	Uncertain significance (Nov 20, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EDDM3B	protein_coding	protein_coding	ENST00000326783	1	2522

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.132	76	79.3	0.958	0.00000378	995
Missense in Polyphen		33	36.263	0.91001		464
Synonymous	-1.47	38	28.1	1.35	0.00000144	242
Loss of Function

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Possible function in sperm maturation.

Recessive Scores

• pRec: 0.117

Intolerance Scores

• loftool: 0.510
• rvis_EVS: 0.48
• rvis_percentile_EVS: 79.04

Haploinsufficiency Scores

• pHI: 0.0690
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• 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: Eddm3b
• Phenotype: vision/eye phenotype; pigmentation phenotype; homeostasis/metabolism phenotype

Gene ontology

• Cellular component: extracellular region
• Molecular function: molecular_function;protein binding