SERGEF

secretion regulating guanine nucleotide exchange factor

Basic information

Region (hg38): 11:17788048-18013047

Links

ENSG00000129158 ∙ NCBI:26297 ∙ OMIM:606051 ∙ HGNC:17499 ∙ Uniprot:Q9UGK8 ∙ 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 SERGEF gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SERGEF 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			25	2		27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	25	2	0

Variants in SERGEF

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

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

Position	Type	Phenotype	Significance	ClinVar
11-17788093-C-G		not specified	Uncertain significance (Mar 25, 2024)
11-17788171-T-C		not specified	Uncertain significance (Dec 27, 2022)
11-17788180-G-C		not specified	Uncertain significance (Mar 31, 2024)
11-17788195-C-T		not specified	Uncertain significance (Apr 25, 2022)
11-17788277-G-T		not specified	Uncertain significance (Jun 24, 2022)
11-17788293-C-T		not specified	Uncertain significance (Dec 17, 2021)
11-17788327-G-C		not specified	Uncertain significance (Aug 22, 2023)
11-17788332-G-A		not specified	Uncertain significance (Jan 03, 2024)
11-17788348-C-T		not specified	Likely benign (Jul 09, 2021)
11-17878214-T-C		not specified	Likely benign (Oct 03, 2022)
11-17878229-C-T		not specified	Uncertain significance (May 26, 2024)
11-17959508-T-A		not specified	Uncertain significance (Oct 05, 2023)
11-17959589-C-A		not specified	Uncertain significance (May 29, 2024)
11-17988605-G-A		not specified	Uncertain significance (Sep 01, 2021)
11-17988609-C-G		not specified	Uncertain significance (Dec 07, 2023)
11-17988628-C-G		not specified	Uncertain significance (Jan 23, 2024)
11-17988675-T-C		not specified	Uncertain significance (Mar 20, 2023)
11-17988683-A-C		not specified	Uncertain significance (Jul 14, 2022)
11-17995804-C-G		not specified	Uncertain significance (Apr 11, 2023)
11-17995806-G-C		not specified	Uncertain significance (Apr 26, 2023)
11-17995858-C-A		not specified	Uncertain significance (Dec 03, 2021)
11-17995859-G-A		not specified	Uncertain significance (Dec 08, 2023)
11-18000557-G-A		not specified	Uncertain significance (Jul 08, 2022)
11-18004506-T-A		not specified	Uncertain significance (Aug 09, 2021)
11-18006626-A-G		not specified	Uncertain significance (Aug 02, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SERGEF	protein_coding	protein_coding	ENST00000265965	11	225115

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.29e-14	0.0533	125169	1	578	125748	0.00230

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.472	217	237	0.914	0.0000116	2933
Missense in Polyphen		57	77.029	0.73998		940
Synonymous	0.780	84	93.6	0.897	0.00000487	912
Loss of Function	0.496	22	24.7	0.892	0.00000130	282

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00338	0.00331
Ashkenazi Jewish	0.00496	0.00497
East Asian	0.000544	0.000544
Finnish	0.000601	0.000601
European (Non-Finnish)	0.00275	0.00275
Middle Eastern	0.000544	0.000544
South Asian	0.00282	0.00281
Other	0.00294	0.00294

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable guanine nucleotide exchange factor (GEF), which may be involved in the secretion process.

Recessive Scores

• pRec: 0.0925

Intolerance Scores

• loftool: 0.559
• rvis_EVS: 0.82
• rvis_percentile_EVS: 87.95

Haploinsufficiency Scores

• pHI: 0.0957
• hipred: N
• hipred_score: 0.258
• ghis: 0.451

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0102

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sergef

Gene ontology

• Biological process: signal transduction;negative regulation of protein secretion
• Cellular component: nucleus;nucleoplasm;cytoplasm;cytosol;aggresome;intracellular membrane-bounded organelle
• Molecular function: Ran guanyl-nucleotide exchange factor activity;protein binding