SERPINA10

protein-coding

serpin family A member 10, the group of Serpin peptidase inhibitors

Gene summary

The protein encoded by this gene belongs to the serpin family. It is predominantly expressed in the liver and secreted in plasma. It inhibits the activity of coagulation factors Xa and XIa in the presence of protein Z, calcium and phospholipid. Mutations in this gene are associated with venous thrombosis. Alternatively spliced transcript variants have been found for this gene.[provided by RefSeq, May 2010]

MANE transcript

NM_001100607.3

Inheritance

—

ClinVar variants

U:60B:7

Top phenotype

LAMB2-related infantile-onset nephrotic syndrome

gnomAD constraint

pLI —, LoF o/e 1.12

Max pathogenic AF

—

Genomic locus

chr14:94,280,460-94,293,268

External References & Databases

Ensembl (ENSG00000140093)

Transcript & Mutation Effects

hg38 • Region Span ~12.8 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 SERPINA10 variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 62

not providedTotal: 3

LAMB2-related infantile-onset nephrotic syndromeTotal: 1

Venous thrombosis, susceptibility toTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001100607.3. 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			56 clinvar	6 clinvar		62
nonsense			1 clinvar	1 clinvar		2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	60	7	0	67

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 52 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001100607.3	RefSeq	NP_001094077.1	4	MANE Select
ENST00000261994.9	Ensembl	ENSP00000261994.4	4	MANE Select
NM_016186.3	RefSeq	NP_057270.1	4	Standard
ENST00000393096.5	Ensembl	ENSP00000376809.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Post-translational protein phosphorylation
Post-translational protein modification
Metabolism of proteins
Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs)

Biological Process

blood coagulation
negative regulation of endopeptidase activity
post-translational protein modification
cellular protein metabolic process
regulation of acrosome reaction

Molecular Function

serine-type endopeptidase inhibitor activity
heparin binding

Cellular Component

extracellular space
endoplasmic reticulum lumen
extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000393096
Coding exons: 4
Length: 9959
Individuals with no LoFs: 122813
Homozygous LoFs: 18
Heterozygous LoFs: 2917
Defined: 125748
p: 0.0117

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.189	244	236	1.03	0.0000123	2927
Missense (PolyPhen)		63	65.362	0.96386		868
Synonymous	0.0255	94	94.3	0.997	0.00000528	864
Loss of Function	-0.417	15	13.4	1.12	5.69e-7	182

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0039	0.0038	notable
Latino/Admixed American	0.0082	0.0082	notable
Ashkenazi Jewish	0.019	0.019	notable
East Asian	0.0022	0.0022	notable
Finnish	0.018	0.017	notable
European (Non-Finnish)	0.012	0.012	notable
South Asian	0.018	0.017	notable
Other	0.016	0.016	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Inhibits activity of the coagulation protease factor Xa in the presence of PROZ, calcium and phospholipids. Also inhibits factor XIa in the absence of cofactors. {ECO:0000269|PubMed:11049983}.;

Recessive Scores

pRec: 0.144

Intolerance Scores

LoFtool: 0.109
RVIS EVS: 2.4
RVIS percentile EVS: 98.51

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.253

Gene Damage Prediction

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