SERPINB9

protein-coding

serpin family B member 9, the group of Serpin peptidase inhibitors

Gene summary

This gene encodes a member of the serine protease inhibitor family which are also known as serpins. The encoded protein belongs to a subfamily of intracellular serpins. This protein inhibits the activity of the effector molecule granzyme B. Overexpression of this protein may prevent cytotoxic T-lymphocytes from eliminating certain tumor cells. A pseudogene of this gene is found on chromosome 6. [provided by RefSeq, Mar 2012]

Previous symbols:

MANE transcript

NM_004155.6

Inheritance

—

ClinVar variants

U:63B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.42

Max pathogenic AF

—

Genomic locus

chr6:2,887,173-2,903,309

External References & Databases

Ensembl (ENSG00000170542)

Transcript & Mutation Effects

hg38 • Region Span ~16.1 kb

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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 SERPINB9 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 61

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_004155.6. 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			2 clinvar	2 clinvar		4
missense			60 clinvar	3 clinvar		63
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	63	5	0	68

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 25 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_004155.6	RefSeq	NP_004146.1	6	MANE Select
ENST00000380698.5	Ensembl	ENSP00000370074.4	6	MANE Select
ENST00000718363.1	Ensembl	ENSP00000520789.1	6	Standard
ENST00000718363.2	Ensembl	ENSP00000520789.1	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Amoebiasis - Homo sapiens (human)
Glucocorticoid Receptor Pathway
Nuclear Receptors Meta-Pathway

Biological Process

mast cell mediated immunity
apoptotic process
immune response
response to bacterium
positive regulation of gene expression

Molecular Function

protease binding
serine-type endopeptidase inhibitor activity
protein binding
cysteine-type endopeptidase inhibitor activity involved in apoptotic process

Cellular Component

extracellular space
nucleus
nucleoplasm
cytoplasm
Golgi apparatus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000380698
Coding exons: 6
Length: 16015
Individuals with no LoFs: 125697
Homozygous LoFs: 0
Heterozygous LoFs: 51
Defined: 125748
p: 0.000203

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.00670	218	218	0.999	0.0000122	2480
Missense (PolyPhen)		69	72.802	0.94778		952
Synonymous	0.721	85	93.9	0.905	0.00000644	723
Loss of Function	1.87	5	12.0	0.418	5.05e-7	148

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.000031	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0.00014	0.00014	rare
European (Non-Finnish)	0.00035	0.00034	rare
South Asian	0.00013	0.00013	rare
Other	0.00034	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Granzyme B inhibitor.;

Recessive Scores

pRec: 0.218

Intolerance Scores

LoFtool: 0.209
RVIS EVS: -0.6
RVIS percentile EVS: 17.91

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.159

Gene Damage Prediction

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