F10

coagulation factor X, the group of Gla domain containing

Basic information

Region (hg38): 13:113122799-113149529

Links

ENSG00000126218 ∙ NCBI:2159 ∙ OMIM:613872 ∙ HGNC:3528 ∙ Uniprot:P00742 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• congenital factor X deficiency (Strong), mode of inheritance: AR
• congenital factor X deficiency (Definitive), mode of inheritance: AR
• congenital factor X deficiency (Supportive), mode of inheritance: AR
• congenital factor X deficiency (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Factor X deficiency	AR	Hematologic; Pharmacogenomic	Individuals can suffer from bleeding diatheses of varying severity, and preventive measures related to bleeding episodes can be beneficial, including in special circumstances such as pregnancy; Precautions should be taken related to certain agents that may provoke/worsen bleeding risk	Hematologic	5450692; 4989292; 4995085; 3732313; 8192155; 3408671; 2567188; 2790181; 1985698; 1997381; 9695984; 10746568; 12028042; 22151249; 22460599; 22506295

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the F10 gene.

• Factor X deficiency (1 variants)
• Hereditary factor X deficiency disease (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the F10 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			5	5	2	12
missense	1	15	40		3	59
nonsense		1	2			3
start loss						0
frameshift	1	3				4
inframe indel						0
splice donor/acceptor (+/-2bp)		1				1
splice region				2		2
non coding			3	1	12	16
Total	2	20	50	6	17

Highest pathogenic variant AF is 0.00000657

Variants in F10

This is a list of pathogenic ClinVar variants found in the F10 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-113122816-C-T		Factor X deficiency • Factor VII deficiency	Benign/Likely benign (Jun 19, 2021)
13-113122846-C-G		Hereditary factor X deficiency disease	Uncertain significance (Jan 12, 2018)
13-113122862-C-T		Hereditary factor X deficiency disease	Uncertain significance (Jan 13, 2018)
13-113122883-C-T		Factor X deficiency	Uncertain significance (Apr 28, 2021)
13-113122885-C-T			Likely benign (Mar 01, 2022)
13-113122887-G-T		Inborn genetic diseases	Uncertain significance (Mar 11, 2024)
13-113122912-G-A		Hereditary factor X deficiency disease	Conflicting classifications of pathogenicity (Jun 01, 2024)
13-113122915-C-T		Factor X deficiency	Conflicting classifications of pathogenicity (Nov 01, 2024)
13-113122926-G-A		F10-related disorder	Likely pathogenic (Aug 06, 2024)
13-113123195-A-G			Benign (Nov 11, 2018)
13-113129397-G-GGGAGCCTGGGTGAAGA			Benign (Jun 20, 2021)
13-113129444-C-T		Hereditary factor X deficiency disease	Benign/Likely benign (Dec 20, 2018)
13-113129458-T-C		Inborn genetic diseases	Uncertain significance (May 05, 2023)
13-113129461-G-A		Factor X deficiency	Uncertain significance (Apr 28, 2021)
13-113129465-G-T		Factor X deficiency	Uncertain significance (Apr 28, 2021)
13-113129470-A-G		Factor X deficiency	Uncertain significance (Apr 28, 2021)
13-113129471-G-C		Hereditary factor X deficiency disease	Benign (Dec 31, 2019)
13-113129488-C-A		Factor X deficiency	Uncertain significance (Apr 28, 2021)
13-113129492-G-A		Hereditary factor X deficiency disease	Benign (Dec 31, 2019)
13-113129500-G-C		Hereditary factor X deficiency disease	Likely pathogenic (-)
13-113129521-A-G		Factor X deficiency	Pathogenic (Nov 08, 1996)
13-113129523-A-C		Hereditary factor X deficiency disease • Inborn genetic diseases	Conflicting classifications of pathogenicity (Oct 05, 2023)
13-113129528-G-A			Likely benign (Jun 08, 2018)
13-113129533-G-A		Factor X deficiency	Uncertain significance (Apr 28, 2021)
13-113129541-G-A		Factor X deficiency • Hereditary factor X deficiency disease	Conflicting classifications of pathogenicity (Feb 01, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
F10	protein_coding	protein_coding	ENST00000375559	8	26716

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000235	0.913	125715	0	33	125748	0.000131

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.20	245	304	0.807	0.0000211	3218
Missense in Polyphen		86	133.73	0.64307		1399
Synonymous	0.461	126	133	0.949	0.0000109	912
Loss of Function	1.67	12	20.0	0.599	9.42e-7	235

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000244	0.000242
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.000237	0.000231
European (Non-Finnish)	0.000115	0.000114
Middle Eastern	0.000109	0.000109
South Asian	0.000196	0.000196
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Factor Xa is a vitamin K-dependent glycoprotein that converts prothrombin to thrombin in the presence of factor Va, calcium and phospholipid during blood clotting.
• Disease: DISEASE: Factor X deficiency (FA10D) [MIM:227600]: A hemorrhagic disease with variable presentation. Affected individuals can manifest prolonged nasal and mucosal hemorrhage, menorrhagia, hematuria, and occasionally hemarthrosis. Some patients do not have clinical bleeding diathesis. {ECO:0000269|PubMed:10468877, ECO:0000269|PubMed:10739379, ECO:0000269|PubMed:10746568, ECO:0000269|PubMed:11248282, ECO:0000269|PubMed:11728527, ECO:0000269|PubMed:12574802, ECO:0000269|PubMed:12945883, ECO:0000269|PubMed:15075089, ECO:0000269|PubMed:15650540, ECO:0000269|PubMed:17393015, ECO:0000269|PubMed:19135706, ECO:0000269|PubMed:1973167, ECO:0000269|PubMed:1985698, ECO:0000269|PubMed:25313940, ECO:0000269|PubMed:26222694, ECO:0000269|PubMed:2790181, ECO:0000269|PubMed:7669671, ECO:0000269|PubMed:7860069, ECO:0000269|PubMed:8529633, ECO:0000269|PubMed:8845463, ECO:0000269|PubMed:8910490}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Complement and coagulation cascades - Homo sapiens (human);Warfarin Pathway, Pharmacodynamics;Aminocaproic Acid Action Pathway;Tranexamic Acid Action Pathway;Urokinase Action Pathway;Reteplase Action Pathway;Streptokinase Action Pathway;Tenecteplase Action Pathway;Alteplase Action Pathway;Anistreplase Action Pathway;Aprotinin Action Pathway;Phenindione Action Pathway;Dicoumarol Action Pathway;Warfarin Action Pathway;Acenocoumarol Action Pathway;Coagulation ;Bivalirudin Action Pathway;Argatroban Action Pathway;Ardeparin Action Pathway;Heparin Action Pathway;Fondaparinux Action Pathway;Enoxaparin Action Pathway;Phenprocoumon Action Pathway;Dicumarol Action Pathway;Ximelagatran Action Pathway;Lepirudin Action Pathway;Blood Clotting Cascade;Human Complement System;Dengue-2 Interactions with Complement and Coagulation Cascades;Dengue-2 Interactions with Blood Clotting Cascade;Complement and Coagulation Cascades;intrinsic prothrombin activation pathway;Post-translational protein modification;Metabolism of proteins;Gamma-carboxylation of protein precursors;Removal of aminoterminal propeptides from gamma-carboxylated proteins;Gamma-carboxylation, transport, and amino-terminal cleavage of proteins;Gamma carboxylation, hypusine formation and arylsulfatase activation;Extrinsic Pathway of Fibrin Clot Formation;Intrinsic Pathway of Fibrin Clot Formation;Hemostasis;Common Pathway of Fibrin Clot Formation;Formation of Fibrin Clot (Clotting Cascade);Beta2 integrin cell surface interactions;extrinsic prothrombin activation pathway (Consensus)

Recessive Scores

• pRec: 0.456

Intolerance Scores

• loftool: 0.107
• rvis_EVS: -0.55
• rvis_percentile_EVS: 19.86

Haploinsufficiency Scores

• pHI: 0.144
• hipred: Y
• hipred_score: 0.645
• ghis: 0.534

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.913

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: F10
• Phenotype: cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype; homeostasis/metabolism phenotype

Zebrafish Information Network

• Gene name: f10
• Affected structure: muscle
• Phenotype tag: abnormal
• Phenotype quality: hemorrhagic

Gene ontology

• Biological process: proteolysis;endoplasmic reticulum to Golgi vesicle-mediated transport;blood coagulation;blood coagulation, extrinsic pathway;positive regulation of cell migration;positive regulation of protein kinase B signaling
• Cellular component: extracellular region;extracellular space;endoplasmic reticulum lumen;Golgi lumen;plasma membrane;intrinsic component of external side of plasma membrane
• Molecular function: serine-type endopeptidase activity;calcium ion binding;protein binding;phospholipid binding