EFR3A

EFR3 homolog A, the group of Armadillo like helical domain containing

Basic information

Region (hg38): 8:131904093-132013642

Links

ENSG00000132294 ∙ NCBI:23167 ∙ OMIM:611798 ∙ HGNC:28970 ∙ Uniprot:Q14156 ∙ 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 EFR3A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EFR3A 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				2		2
missense			63	1		64
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	64	3	0

Variants in EFR3A

This is a list of pathogenic ClinVar variants found in the EFR3A region.

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

Position	Type	Phenotype	Significance	ClinVar
8-131940503-A-G			Likely benign (Oct 01, 2022)
8-131940520-C-T		not specified	Uncertain significance (Mar 01, 2023)
8-131940525-C-T		not specified	Uncertain significance (May 11, 2022)
8-131940526-G-A		not specified	Uncertain significance (Sep 14, 2022)
8-131940540-C-T		not specified	Uncertain significance (Mar 16, 2022)
8-131940558-T-C		not specified	Uncertain significance (Jan 28, 2025)
8-131944763-G-A		not specified	Uncertain significance (Nov 16, 2024)
8-131944763-G-C		not specified	Uncertain significance (Jun 29, 2022)
8-131944796-G-A		not specified	Uncertain significance (Jun 28, 2024)
8-131946516-A-C		not specified	Uncertain significance (Apr 20, 2024)
8-131946572-A-G		EFR3A-related disorder	Benign (Mar 19, 2019)
8-131946604-C-A		not specified	Uncertain significance (Dec 31, 2023)
8-131946604-C-T		not specified	Uncertain significance (Nov 09, 2024)
8-131946605-C-A		not specified	Uncertain significance (Nov 17, 2023)
8-131950018-G-A		not specified	Uncertain significance (Jun 02, 2023)
8-131950039-G-A		not specified	Uncertain significance (Aug 28, 2023)
8-131953798-CTT-C		EFR3A-related disorder	Benign (May 03, 2019)
8-131953818-G-T		EFR3A-related disorder	Uncertain significance (Mar 01, 2024)
8-131953850-G-A		not specified	Uncertain significance (Feb 03, 2022)
8-131953872-C-T		EFR3A-related disorder	Benign (Aug 24, 2021)
8-131953882-C-T		not specified	Uncertain significance (Aug 14, 2024)
8-131953918-A-T		not specified	Uncertain significance (Nov 23, 2024)
8-131953920-T-G		EFR3A-related disorder	Benign (Jul 02, 2019)
8-131953943-T-C		not specified	Uncertain significance (Nov 21, 2024)
8-131955765-T-C		EFR3A-related disorder	Benign (May 03, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EFR3A	protein_coding	protein_coding	ENST00000254624	23	109555

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.81e-11	0.997	125542	0	51	125593	0.000203

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.796	376	422	0.891	0.0000221	5366
Missense in Polyphen		84	121.19	0.69312		1510
Synonymous	-0.169	142	139	1.02	0.00000713	1535
Loss of Function	2.78	24	43.9	0.547	0.00000255	537

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000672	0.000670
Ashkenazi Jewish	0.00	0.00
East Asian	0.000112	0.000109
Finnish	0.000186	0.000185
European (Non-Finnish)	0.000254	0.000220
Middle Eastern	0.000112	0.000109
South Asian	0.000136	0.000131
Other	0.000333	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of a complex required to localize phosphatidylinositol 4-kinase (PI4K) to the plasma membrane (PubMed:23229899, PubMed:25608530, PubMed:26571211). The complex acts as a regulator of phosphatidylinositol 4-phosphate (PtdIns(4)P) synthesis (Probable). In the complex, EFR3A probably acts as the membrane-anchoring component (PubMed:23229899). Also involved in responsiveness to G-protein-coupled receptors; it is however unclear whether this role is direct or indirect (PubMed:25380825). {ECO:0000269|PubMed:23229899, ECO:0000269|PubMed:25380825, ECO:0000269|PubMed:25608530, ECO:0000305}.
• Disease: DISEASE: Note=Genetic variations in EFR3A may be associated with susceptibility to autism. {ECO:0000305|PubMed:24860643}.

Recessive Scores

• pRec: 0.0879

Intolerance Scores

• loftool: 0.923
• rvis_EVS: -0.31
• rvis_percentile_EVS: 32.23

Haploinsufficiency Scores

• pHI: 0.0810
• hipred: N
• hipred_score: 0.492
• ghis: 0.563

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.218

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Efr3a

Gene ontology

• Biological process: phosphatidylinositol phosphorylation;protein localization to plasma membrane
• Cellular component: cytosol;plasma membrane