EFR3B

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

Basic information

Region (hg38): 2:25042075-25159135

Previous symbols: [ "KIAA0953" ]

Links

ENSG00000084710 ∙ NCBI:22979 ∙ OMIM:616797 ∙ HGNC:29155 ∙ Uniprot:Q9Y2G0 ∙ 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 EFR3B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EFR3B 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			36			36
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	36	0	0

Variants in EFR3B

This is a list of pathogenic ClinVar variants found in the EFR3B region.

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

Position	Type	Phenotype	Significance	ClinVar
2-25091399-G-A		not specified	Uncertain significance (May 02, 2024)
2-25093043-A-G		not specified	Uncertain significance (Sep 29, 2023)
2-25093081-G-A		not specified	Uncertain significance (Dec 19, 2022)
2-25093095-G-C		not specified	Uncertain significance (Aug 16, 2021)
2-25093105-C-T		not specified	Uncertain significance (Dec 05, 2022)
2-25121694-G-A		not specified	Uncertain significance (May 31, 2023)
2-25121764-C-T		not specified	Uncertain significance (Mar 06, 2023)
2-25121791-C-A		not specified	Uncertain significance (Oct 06, 2021)
2-25130108-A-G		not specified	Uncertain significance (Aug 12, 2021)
2-25130562-A-T		not specified	Uncertain significance (Dec 19, 2023)
2-25131389-A-C		not specified	Uncertain significance (May 27, 2022)
2-25131455-G-A		not specified	Uncertain significance (Apr 09, 2024)
2-25131821-G-T		not specified	Uncertain significance (Sep 17, 2021)
2-25131854-A-G		not specified	Uncertain significance (Nov 21, 2022)
2-25132992-G-A		not specified	Uncertain significance (Dec 12, 2022)
2-25133013-G-A		not specified	Uncertain significance (Aug 17, 2022)
2-25135600-T-C		not specified	Uncertain significance (Jul 20, 2022)
2-25136581-A-G		not specified	Uncertain significance (Dec 27, 2023)
2-25136584-G-A		not specified	Uncertain significance (Sep 21, 2021)
2-25137357-A-G		not specified	Uncertain significance (Mar 12, 2024)
2-25137414-C-T		not specified	Uncertain significance (Jul 06, 2021)
2-25137482-C-T		not specified	Uncertain significance (Jan 10, 2023)
2-25137488-G-C		not specified	Uncertain significance (Jan 26, 2022)
2-25137495-C-T		not specified	Uncertain significance (Dec 21, 2022)
2-25139061-C-A		not specified	Uncertain significance (Oct 20, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EFR3B	protein_coding	protein_coding	ENST00000403714	23	113245

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0241	0.976	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	4.26	228	495	0.461	0.0000308	5347
Missense in Polyphen		80	189.22	0.42279		2078
Synonymous	3.56	135	199	0.679	0.0000128	1576
Loss of Function	4.52	12	44.6	0.269	0.00000233	513

LoF frequencies by population

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

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, EFR3B 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:0000269|PubMed:26571211, ECO:0000305}.

Intolerance Scores

• rvis_EVS: -0.4
• rvis_percentile_EVS: 26.53

Haploinsufficiency Scores

• pHI: 0.135
• ghis: 0.626

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: Efr3b

Gene ontology

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