SERPINB13

serpin family B member 13, the group of Serpin peptidase inhibitors

Basic information

Region (hg38): 18:63586988-63604639

Previous symbols: [ "PI13" ]

Links

ENSG00000197641 ∙ NCBI:5275 ∙ OMIM:604445 ∙ HGNC:8944 ∙ Uniprot:Q9UIV8 ∙ 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 SERPINB13 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SERPINB13 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					1	1
missense			28	1		29
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	28	1	1

Variants in SERPINB13

This is a list of pathogenic ClinVar variants found in the SERPINB13 region.

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

Position	Type	Phenotype	Significance	ClinVar
18-63588773-A-T		not specified	Uncertain significance (May 24, 2023)
18-63588815-G-C		not specified	Uncertain significance (Jun 11, 2021)
18-63588815-G-T		not specified	Uncertain significance (Jul 19, 2023)
18-63589678-C-T		not specified	Uncertain significance (Aug 10, 2021)
18-63589679-G-A			Benign (Dec 31, 2018)
18-63589711-A-T		not specified	Uncertain significance (Sep 28, 2021)
18-63592373-A-T		not specified	Uncertain significance (Dec 28, 2022)
18-63592457-A-G		not specified	Uncertain significance (Jun 21, 2022)
18-63592879-A-G		not specified	Uncertain significance (May 17, 2023)
18-63592894-T-C		not specified	Uncertain significance (Feb 12, 2024)
18-63592906-A-G		not specified	Uncertain significance (Dec 19, 2022)
18-63594396-T-C		not specified	Uncertain significance (Jan 16, 2024)
18-63594435-G-A		not specified	Uncertain significance (Oct 12, 2021)
18-63594466-A-G		not specified	Uncertain significance (Feb 07, 2023)
18-63594479-G-T		not specified	Uncertain significance (Mar 11, 2022)
18-63594483-T-C		not specified	Uncertain significance (Mar 04, 2024)
18-63595060-A-G		not specified	Uncertain significance (Mar 01, 2023)
18-63595079-C-G		not specified	Uncertain significance (Nov 10, 2022)
18-63595104-A-C		not specified	Uncertain significance (Sep 27, 2022)
18-63595113-G-A		not specified	Uncertain significance (Feb 13, 2023)
18-63595134-G-A		not specified	Uncertain significance (Dec 27, 2023)
18-63596975-G-A		not specified	Uncertain significance (Jun 03, 2022)
18-63597024-A-T		not specified	Uncertain significance (Apr 05, 2023)
18-63597026-A-G		not specified	Likely benign (Dec 03, 2021)
18-63597070-G-A		not specified	Uncertain significance (Nov 07, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SERPINB13	protein_coding	protein_coding	ENST00000344731	7	17651

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000702	0.737	125685	3	60	125748	0.000251

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.541	235	213	1.10	0.0000108	2617
Missense in Polyphen		88	82.486	1.0669		1095
Synonymous	-0.0484	86	85.4	1.01	0.00000518	713
Loss of Function	1.14	10	14.7	0.679	8.41e-7	169

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000495	0.000485
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.000598	0.000598
Finnish	0.0000465	0.0000462
European (Non-Finnish)	0.000142	0.000141
Middle Eastern	0.000598	0.000598
South Asian	0.000886	0.000784
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in the proliferation or differentiation of keratinocytes.
• Pathway: Amoebiasis - Homo sapiens (human);Transcriptional regulation by RUNX1;Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription;RUNX1 regulates transcription of genes involved in differentiation of keratinocytes;Transcriptional regulation by RUNX1 (Consensus)

Recessive Scores

• pRec: 0.127

Intolerance Scores

• loftool: 0.204
• rvis_EVS: -0.4
• rvis_percentile_EVS: 26.73

Haploinsufficiency Scores

• pHI: 0.116
• hipred: N
• hipred_score: 0.112
• ghis: 0.499

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0103

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Serpinb13

Gene ontology

• Biological process: response to UV;negative regulation of endopeptidase activity;regulation of proteolysis;regulation of keratinocyte differentiation;negative regulation of keratinocyte apoptotic process
• Cellular component: extracellular space;nucleoplasm;nucleolus;cytoplasm;cytosol;nuclear speck;lysosomal lumen;extracellular exosome
• Molecular function: protease binding;serine-type endopeptidase inhibitor activity;cysteine-type endopeptidase inhibitor activity