IPCEF1

interaction protein for cytohesin exchange factors 1, the group of Pleckstrin homology domain containing

Basic information

Region (hg38): 6:154154495-154356803

Links

ENSG00000074706 ∙ NCBI:26034 ∙ OMIM:619948 ∙ HGNC:21204 ∙ Uniprot:Q8WWN9 ∙ 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 IPCEF1 gene.

• Inborn genetic diseases (5 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IPCEF1 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			4	1	1	6
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	4	1	2

Variants in IPCEF1

This is a list of pathogenic ClinVar variants found in the IPCEF1 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-154159833-T-C		not specified	Uncertain significance (Jun 21, 2022)
6-154166286-C-T			Benign (Mar 14, 2018)
6-154168101-A-C		not specified	Uncertain significance (Jul 27, 2022)
6-154200025-A-G			Benign (Jun 27, 2018)
6-154214233-T-A		not specified	Uncertain significance (Dec 08, 2023)
6-154214248-T-G		not specified	Uncertain significance (Feb 10, 2022)
6-154214256-G-A		not specified	Likely benign (Feb 15, 2023)
6-154246511-T-C		Tramadol response	drug response (Apr 28, 2018)
6-154246532-T-G		Tramadol response	drug response (Apr 28, 2018)
6-154246542-G-A		Tramadol response	drug response (Apr 28, 2018)
6-154246546-C-T		Tramadol response	drug response (Apr 28, 2018)
6-154246692-G-A		Tramadol response	drug response (Apr 28, 2018)
6-154246729-C-T		Tramadol response	drug response (Apr 28, 2018)
6-154246798-C-T		Tramadol response	drug response (Apr 28, 2018)
6-154246823-C-T		Tramadol response	drug response (Apr 28, 2018)
6-154246824-C-T		Tramadol response	drug response (Apr 28, 2018)
6-154246833-G-T		Tramadol response	drug response (Apr 28, 2018)
6-154246874-G-T		Tramadol response	drug response (Apr 28, 2018)
6-154246891-C-T		Tramadol response	drug response (Apr 28, 2018)
6-154246902-CA-C		Tramadol response	drug response (Apr 28, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IPCEF1	protein_coding	protein_coding	ENST00000422970	10	202296

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00156	0.997	125730	0	15	125745	0.0000596

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.23	179	232	0.772	0.0000117	2875
Missense in Polyphen		38	72.702	0.52268		919
Synonymous	0.506	85	91.1	0.933	0.00000500	818
Loss of Function	2.83	9	24.0	0.376	0.00000128	284

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000869	0.0000869
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000796	0.0000791
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000353	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Enhances the promotion of guanine-nucleotide exchange by PSCD2 on ARF6 in a concentration-dependent manner. {ECO:0000250}.
• Pathway: Arf6 signaling events (Consensus)

Intolerance Scores

• loftool: 0.544
• rvis_EVS: 0.33
• rvis_percentile_EVS: 73.41

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.542
• ghis: 0.588

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.902

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ipcef1

Gene ontology

• Biological process: response to oxidative stress;oxygen transport;cellular oxidant detoxification
• Cellular component: cytosol;plasma membrane
• Molecular function: peroxidase activity;oxygen carrier activity;protein binding;protein domain specific binding