EDDM3A

epididymal protein 3A

Basic information

Region (hg38): 14:20745886-20748380

Previous symbols: [ "FAM12A" ]

Links

ENSG00000181562 ∙ NCBI:10876 ∙ OMIM:611580 ∙ HGNC:16978 ∙ Uniprot:Q14507 ∙ 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 EDDM3A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EDDM3A 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			12	1		13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	1	0

Variants in EDDM3A

This is a list of pathogenic ClinVar variants found in the EDDM3A region.

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

Position	Type	Phenotype	Significance	ClinVar
14-20747588-C-T		not specified	Uncertain significance (May 03, 2023)
14-20747608-A-G		not specified	Uncertain significance (Dec 15, 2023)
14-20747611-C-A		not specified	Uncertain significance (Aug 19, 2023)
14-20747657-A-G		not specified	Uncertain significance (Apr 17, 2023)
14-20747670-G-C		not specified	Uncertain significance (Feb 21, 2024)
14-20747708-G-A		not specified	Uncertain significance (Sep 20, 2023)
14-20747780-T-C		not specified	Uncertain significance (Jan 27, 2022)
14-20747812-C-T		not specified	Uncertain significance (Aug 02, 2021)
14-20747819-G-A		not specified	Uncertain significance (May 22, 2024)
14-20747837-G-A		not specified	Uncertain significance (May 08, 2023)
14-20747890-G-A		not specified	Likely benign (Jul 13, 2021)
14-20747930-G-A		not specified	Uncertain significance (Apr 04, 2024)
14-20747933-G-A		not specified	Uncertain significance (Apr 26, 2024)
14-20747961-T-G		not specified	Uncertain significance (Jan 18, 2023)
14-20747969-A-G		not specified	Uncertain significance (Jul 06, 2021)
14-20747978-T-C		not specified	Uncertain significance (Dec 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EDDM3A	protein_coding	protein_coding	ENST00000326842	1	2489

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	-0.108	83	80.3	1.03	0.00000395	983
Missense in Polyphen		21	25.121	0.83596		331
Synonymous	-2.10	42	27.9	1.51	0.00000136	245
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.

Intolerance Scores

• loftool: 0.777
• rvis_EVS: 0.88
• rvis_percentile_EVS: 89.02

Haploinsufficiency Scores

• pHI: 0.0927
• 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

• Biological process: sperm displacement
• Cellular component: extracellular space