SERPINA9

protein-coding

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

Gene summary

Enables serine-type endopeptidase inhibitor activity. Predicted to be located in cytoplasm; extracellular region; and membrane. Predicted to be active in obsolete extracellular space. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_175739.4

Inheritance

—

ClinVar variants

U:93B:7

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.39

Max pathogenic AF

—

Genomic locus

chr14:94,462,717-94,479,689

External References & Databases

Ensembl (ENSG00000170054)

Transcript & Mutation Effects

hg38 • Region Span ~17.0 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 SERPINA9 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 96

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_175739.4. 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						0
missense			91 clinvar	6 clinvar	1 clinvar	98
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	93	6	1	100

Loading ClinVar variants...

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_175739.4	RefSeq	NP_783866.3	4	MANE Select
ENST00000674397.2	Ensembl	ENSP00000501517.1	4	MANE Select
NM_001042518.2	RefSeq	NP_001035983.2	5	Standard
NM_001284275.2	RefSeq	NP_001271204.2	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

negative regulation of endopeptidase activity

Molecular Function

serine-type endopeptidase inhibitor activity

Cellular Component

extracellular space
cytoplasm
membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000337425
Coding exons: 5
Length: 16973
Individuals with no LoFs: 121433
Homozygous LoFs: 73
Heterozygous LoFs: 3319
Defined: 124825
p: 0.0137

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-1.11	275	228	1.21	0.0000112	2851
Missense (PolyPhen)		73	66.714	1.0942		903
Synonymous	-1.95	116	92.2	1.26	0.00000479	873
Loss of Function	-1.26	17	12.2	1.39	5.19e-7	158

Population LoF Frequency

Population	CAF	p-value	Status
African	0.14	0.14	notable
Latino/Admixed American	0.012	0.012	notable
Ashkenazi Jewish	0.019	0.018	notable
East Asian	0.00083	0.00083	rare
Finnish	0.0016	0.0016	notable
European (Non-Finnish)	0.0055	0.0055	notable
South Asian	0.00079	0.00078	rare
Other	0.013	0.012	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Protease inhibitor that inhibits trypsin and trypsin- like serine proteases (in vitro). Inhibits plasmin and thrombin with lower efficiency (in vitro). {ECO:0000269|PubMed:17447896}.;

Recessive Scores

pRec: 0.0945

Intolerance Scores

LoFtool: 0.111
RVIS EVS: 2.78
RVIS percentile EVS: 99.02

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0537

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High