SERBP1

SERPINE1 mRNA binding protein 1

Basic information

Region (hg38): 1:67407809-67430415

Links

ENSG00000142864 ∙ NCBI:26135 ∙ OMIM:607378 ∙ HGNC:17860 ∙ Uniprot:Q8NC51 ∙ 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 SERBP1 gene.

• Inborn genetic diseases (15 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SERBP1 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			15			15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	0	0

Variants in SERBP1

This is a list of pathogenic ClinVar variants found in the SERBP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-67415170-T-C		not specified	Uncertain significance (Dec 28, 2023)
1-67415263-T-C		not specified	Uncertain significance (May 04, 2022)
1-67415338-G-A		not specified	Uncertain significance (Jan 04, 2022)
1-67420119-T-G		not specified	Uncertain significance (Mar 01, 2023)
1-67420171-T-G		not specified	Uncertain significance (Jan 26, 2022)
1-67420185-C-T		not specified	Uncertain significance (Aug 17, 2022)
1-67424209-G-T		not specified	Uncertain significance (Jun 10, 2022)
1-67424228-G-C		not specified	Uncertain significance (Jul 14, 2021)
1-67424242-G-T		not specified	Uncertain significance (Jan 11, 2023)
1-67424263-G-A		not specified	Uncertain significance (Mar 04, 2024)
1-67424285-T-C		not specified	Uncertain significance (Nov 30, 2021)
1-67424904-C-T		not specified	Uncertain significance (Dec 15, 2022)
1-67425119-T-C		not specified	Uncertain significance (Dec 12, 2023)
1-67425146-C-A		not specified	Uncertain significance (Apr 18, 2023)
1-67425221-G-A		not specified	Uncertain significance (Jun 22, 2023)
1-67426207-C-T		not specified	Uncertain significance (Apr 13, 2022)
1-67430017-G-A		not specified	Uncertain significance (Oct 05, 2023)
1-67430098-T-C		not specified	Uncertain significance (Aug 17, 2022)
1-67430116-T-G		not specified	Uncertain significance (Oct 06, 2023)
1-67430193-G-T		not specified	Uncertain significance (Dec 07, 2023)
1-67430249-C-G		not specified	Uncertain significance (Dec 13, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SERBP1	protein_coding	protein_coding	ENST00000370995	8	22606

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000501	124691	0	4	124695	0.0000160

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.67	178	253	0.705	0.0000149	2664
Missense in Polyphen		37	78.788	0.46962		936
Synonymous	-0.868	96	85.8	1.12	0.00000452	802
Loss of Function	4.57	1	26.3	0.0381	0.00000198	247

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)	0.0000269	0.0000265
Middle Eastern	0.00	0.00
South Asian	0.0000381	0.0000330
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in the regulation of mRNA stability. Binds to the 3'-most 134 nt of the SERPINE1/PAI1 mRNA, a region which confers cyclic nucleotide regulation of message decay. {ECO:0000269|PubMed:11001948}.
• Pathway: Apoptosis-related network due to altered Notch3 in ovarian cancer (Consensus)

Recessive Scores

• pRec: 0.179

Intolerance Scores

• loftool: 0.0209
• rvis_EVS: -0.34
• rvis_percentile_EVS: 30.07

Haploinsufficiency Scores

• pHI: 0.670
• hipred: Y
• hipred_score: 0.726
• ghis: 0.724

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.970

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Serbp1

Gene ontology

• Biological process: regulation of apoptotic process;regulation of mRNA stability
• Cellular component: nucleus;cytoplasm;cytosol;plasma membrane;membrane;perinuclear region of cytoplasm;extracellular exosome
• Molecular function: RNA binding;mRNA 3'-UTR binding;protein binding;cadherin binding