SERPINB13

protein-coding

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

Gene summary

The protein encoded by this gene is a member of the serpin family of serine protease inhibitors. The encoded protein inhibits the activity of cathepsin K and is itself transcriptionally repressed by RUNX1. This gene is downregulated in many types of cancer. [provided by RefSeq, Jan 2017]

Previous symbols:

PI13

MANE transcript

NM_012397.4

Inheritance

—

ClinVar variants

U:70B:4

Top phenotype

Prostate cancer

gnomAD constraint

pLI —, LoF o/e 0.68

Max pathogenic AF

—

Genomic locus

chr18:63,586,989-63,604,639

External References & Databases

Ensembl (ENSG00000197641)

Transcript & Mutation Effects

hg38 • Region Span ~17.7 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SERPINB13 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 71

not providedTotal: 1

Prostate cancerTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_012397.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous					1 clinvar	1
missense			69 clinvar	3 clinvar		72
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	70	3	1	74

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 14 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_012397.4	RefSeq	NP_036529.1	7	MANE Select
ENST00000344731.10	Ensembl	ENSP00000341584.6	7	MANE Select
NM_001307923.2	RefSeq	NP_001294852.1	7	Standard
NM_001348267.2	RefSeq	NP_001335196.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Amoebiasis - Homo sapiens (human)
Transcriptional regulation by RUNX1
Gene expression (Transcription)
Generic Transcription Pathway
RNA Polymerase II Transcription

Biological Process

response to UV
negative regulation of endopeptidase activity
regulation of proteolysis
regulation of keratinocyte differentiation
negative regulation of keratinocyte apoptotic process

Molecular Function

protease binding
serine-type endopeptidase inhibitor activity
cysteine-type endopeptidase inhibitor activity

Cellular Component

extracellular space
nucleoplasm
nucleolus
cytoplasm
cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000344731
Coding exons: 7
Length: 17651
Individuals with no LoFs: 125685
Homozygous LoFs: 3
Heterozygous LoFs: 60
Defined: 125748
p: 0.000251

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.541	235	213	1.10	0.0000108	2617
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00038	0.00037	rare
Latino/Admixed American	0.00012	0.00012	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.00060	0.00060	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00014	0.00014	rare
South Asian	0.00089	0.00078	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May play a role in the proliferation or differentiation of keratinocytes.;

Recessive Scores

pRec: 0.127

Intolerance Scores

LoFtool: 0.204
RVIS EVS: -0.4
RVIS percentile EVS: 26.73

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0103

Gene Damage Prediction

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