F13A1

coagulation factor XIII A chain, the group of MicroRNA protein coding host genes|Transglutaminases

Basic information

Region (hg38): 6:6144083-6321013

Previous symbols: [ "F13A" ]

Links

ENSG00000124491 ∙ NCBI:2162 ∙ OMIM:134570 ∙ HGNC:3531 ∙ Uniprot:P00488 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• congenital factor XIII deficiency (Supportive), mode of inheritance: AR
• factor XIII, A subunit, deficiency of (Definitive), mode of inheritance: AR
• factor XIII, A subunit, deficiency of (Definitive), mode of inheritance: AR
• factor XIII, A subunit, deficiency of (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Factor XIIIA deficiency	AR	Hematologic; Pharmacogenomic	Individuals have increased bleeding and poor wound healing; awareness and management of bleeding risk in certain situations (eg, obstetric event or surgery) may decrease morbidity; Precautions should be taken related to certain agents that may provoke/worsen bleeding risk	Hematologic	1644910; 8025280; 7727776; 8547636; 9459313; 10365735; 12072871; 12456499; 17393027; 19438481; 20108427; 21512576

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the F13A1 gene.

• Factor XIII, A subunit, deficiency of (100 variants)
• not provided (68 variants)
• Inborn genetic diseases (29 variants)
• not specified (20 variants)
• F13A1-related condition (3 variants)
• Thrombophilia due to thrombin defect (2 variants)
• Factor XIII, A subunit, deficiency of;Thrombophilia due to thrombin defect;Myocardial infarction, susceptibility to (1 variants)
• Venous thrombosis, protection against (1 variants)
• Myocardial infarction, protection against (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the F13A1 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			8	7	2	17
missense	1	4	53	5	2	65
nonsense	2	3				5
start loss						0
frameshift	3	1				4
inframe indel						0
splice donor/acceptor (+/-2bp)	3	1				4
splice region			1	3	2	6
non coding			27	2	41	70
Total	9	9	88	14	45

Highest pathogenic variant AF is 0.000230

Variants in F13A1

This is a list of pathogenic ClinVar variants found in the F13A1 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-6144164-C-G		Factor XIII, A subunit, deficiency of	Uncertain significance (Jan 12, 2018)
6-6144366-A-G		Factor XIII, A subunit, deficiency of	Uncertain significance (Jan 17, 2018)
6-6144452-A-C		Factor XIII, A subunit, deficiency of	Uncertain significance (Jan 13, 2018)
6-6144484-C-T		Factor XIII, A subunit, deficiency of	Uncertain significance (Jan 12, 2018)
6-6144574-G-C		Factor XIII, A subunit, deficiency of	Uncertain significance (Jan 13, 2018)
6-6144589-C-A		Factor XIII, A subunit, deficiency of	Uncertain significance (Jan 12, 2018)
6-6144624-C-A		Factor XIII, A subunit, deficiency of	Benign (Jan 12, 2018)
6-6144653-C-A		Factor XIII, A subunit, deficiency of	Uncertain significance (Jan 12, 2018)
6-6144674-A-G		Factor XIII, A subunit, deficiency of	Uncertain significance (Jan 12, 2018)
6-6144685-C-T		Factor XIII, A subunit, deficiency of	Uncertain significance (Jan 12, 2018)
6-6144692-C-T		Factor XIII, A subunit, deficiency of	Uncertain significance (Jan 12, 2018)
6-6144823-C-T		Factor XIII, A subunit, deficiency of	Uncertain significance (Jan 13, 2018)
6-6144876-C-T		Factor XIII, A subunit, deficiency of	Benign (Jan 13, 2018)
6-6144991-C-T		Factor XIII, A subunit, deficiency of	Uncertain significance (Jan 13, 2018)
6-6144992-C-T		Factor XIII, A subunit, deficiency of	Uncertain significance (Jan 12, 2018)
6-6145000-G-A		Factor XIII, A subunit, deficiency of	Uncertain significance (Jan 13, 2018)
6-6145013-A-G		Factor XIII, A subunit, deficiency of	Uncertain significance (Jan 13, 2018)
6-6145032-C-T		Factor XIII, A subunit, deficiency of	Uncertain significance (Jan 13, 2018)
6-6145176-C-T		Factor XIII, A subunit, deficiency of	Likely benign (Jan 12, 2018)
6-6145191-G-T		Factor XIII, A subunit, deficiency of	Uncertain significance (Jan 12, 2018)
6-6145202-C-A		Factor XIII, A subunit, deficiency of	Uncertain significance (Jan 12, 2018)
6-6145349-G-A		Factor XIII, A subunit, deficiency of	Uncertain significance (Jan 13, 2018)
6-6145398-C-T		Factor XIII, A subunit, deficiency of	Benign (Jan 13, 2018)
6-6145411-A-G		Factor XIII, A subunit, deficiency of	Uncertain significance (Jan 13, 2018)
6-6145459-C-T		Factor XIII, A subunit, deficiency of	Benign (Nov 11, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
F13A1	protein_coding	protein_coding	ENST00000264870	14	176929

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.29e-8	0.998	125640	0	108	125748	0.000430

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.05	356	416	0.855	0.0000248	4826
Missense in Polyphen		125	173.55	0.72027		2068
Synonymous	-0.773	175	162	1.08	0.0000104	1409
Loss of Function	2.79	18	36.1	0.498	0.00000190	417

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000481	0.000481
Ashkenazi Jewish	0.00	0.00
East Asian	0.000218	0.000217
Finnish	0.00203	0.00203
European (Non-Finnish)	0.000388	0.000352
Middle Eastern	0.000218	0.000217
South Asian	0.000261	0.000261
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Factor XIII is activated by thrombin and calcium ion to a transglutaminase that catalyzes the formation of gamma-glutamyl- epsilon-lysine cross-links between fibrin chains, thus stabilizing the fibrin clot. Also cross-link alpha-2-plasmin inhibitor, or fibronectin, to the alpha chains of fibrin. {ECO:0000269|PubMed:27363989}.
• Disease: DISEASE: Factor XIII subunit A deficiency (FA13AD) [MIM:613225]: An autosomal recessive hematologic disorder characterized by a life-long bleeding tendency, impaired wound healing and spontaneous abortion in affected women. {ECO:0000269|PubMed:1353995, ECO:0000269|PubMed:20179087, ECO:0000269|PubMed:24286209, ECO:0000269|PubMed:24329762, ECO:0000269|PubMed:24889649, ECO:0000269|PubMed:27363989}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Complement and coagulation cascades - Homo sapiens (human);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;Human Complement System;Interleukin-4 and 13 signaling;Platelet degranulation ;Response to elevated platelet cytosolic Ca2+;Platelet activation, signaling and aggregation;Hemostasis;Common Pathway of Fibrin Clot Formation;Formation of Fibrin Clot (Clotting Cascade);Alpha9 beta1 integrin signaling events;Beta1 integrin cell surface interactions (Consensus)

Recessive Scores

• pRec: 0.592

Intolerance Scores

• loftool: 0.183
• rvis_EVS: 0.25
• rvis_percentile_EVS: 69.66

Haploinsufficiency Scores

• pHI: 0.336
• hipred: Y
• hipred_score: 0.782
• ghis: 0.421

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.739

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: F13a1
• Phenotype: endocrine/exocrine gland phenotype; homeostasis/metabolism 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; respiratory system phenotype

Gene ontology

• Biological process: platelet degranulation;blood coagulation;peptide cross-linking;cytokine-mediated signaling pathway;blood coagulation, fibrin clot formation
• Cellular component: extracellular region;platelet alpha granule lumen;collagen-containing extracellular matrix;blood microparticle
• Molecular function: protein-glutamine gamma-glutamyltransferase activity;metal ion binding