F13B

coagulation factor XIII B chain, the group of Sushi domain containing

Basic information

Region (hg38): 1:197038741-197067260

Links

ENSG00000143278 ∙ NCBI:2165 ∙ OMIM:134580 ∙ HGNC:3534 ∙ Uniprot:P05160 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

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

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Factor XIIIB 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	2334637; 8324218; 11313256; 20331752; 21640452

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the F13B gene.

• Factor XIII, b subunit, deficiency of (3 variants)
• Coagulation factor deficiency syndrome (1 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the F13B 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	1	2	8
missense			53	2	1	56
nonsense	2					2
start loss						0
frameshift	2	1	1			4
inframe indel			1			1
splice donor/acceptor (+/-2bp)		1				1
splice region			1			1
non coding			3	2	14	19
Total	4	2	63	5	17

Highest pathogenic variant AF is 0.00000658

Variants in F13B

This is a list of pathogenic ClinVar variants found in the F13B region.

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

Position	Type	Phenotype	Significance	ClinVar
1-197039216-G-T		Factor XIII, b subunit, deficiency of	Uncertain significance (Jan 12, 2018)
1-197039235-C-T		Factor XIII, b subunit, deficiency of	Benign (Nov 10, 2018)
1-197039289-C-G		Factor XIII, b subunit, deficiency of	Likely benign (Jan 12, 2018)
1-197039384-TC-T			Uncertain significance (May 27, 2022)
1-197039403-G-A		Factor XIII, b subunit, deficiency of • F13B-related disorder	Uncertain significance (Jan 13, 2018)
1-197039467-A-C			Benign (Jun 18, 2021)
1-197040378-G-C			Benign (Nov 12, 2018)
1-197040532-G-A		Factor XIII, b subunit, deficiency of	Uncertain significance (Aug 06, 2018)
1-197040539-T-A		Factor XIII, b subunit, deficiency of • not specified • F13B-related disorder	Uncertain significance (Dec 01, 2023)
1-197040572-C-T		Factor XIII, b subunit, deficiency of • F13B-related disorder	Uncertain significance (Jan 12, 2018)
1-197040592-T-A		Inborn genetic diseases	Uncertain significance (Oct 05, 2023)
1-197040597-T-C		Factor XIII, b subunit, deficiency of	Uncertain significance (Jan 13, 2018)
1-197040649-C-T		Inborn genetic diseases	Uncertain significance (Aug 02, 2023)
1-197040659-G-A		Factor XIII, b subunit, deficiency of	Conflicting classifications of pathogenicity (Aug 01, 2022)
1-197040668-A-G		not specified • Factor XIII, b subunit, deficiency of	Benign (Aug 10, 2021)
1-197040668-AT-GA		F13B-related disorder	Uncertain significance (Jun 10, 2024)
1-197040668-ATTG-GTT		not specified	Uncertain significance (Jun 02, 2023)
1-197040711-T-G		Inborn genetic diseases	Uncertain significance (Apr 07, 2023)
1-197040720-G-C		Inborn genetic diseases	Uncertain significance (Dec 21, 2022)
1-197040740-GAAC-G		Factor XIII, b subunit, deficiency of	Conflicting classifications of pathogenicity (Mar 01, 2022)
1-197050728-A-C		Factor XIII, b subunit, deficiency of	Benign/Likely benign (Dec 31, 2019)
1-197050735-C-G		Thrombus	Uncertain significance (-)
1-197050742-C-T		Factor XIII, b subunit, deficiency of	Uncertain significance (Apr 28, 2021)
1-197050765-T-C		Factor XIII, b subunit, deficiency of	Uncertain significance (Oct 25, 2024)
1-197050834-A-G		Inborn genetic diseases	Uncertain significance (Oct 05, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
F13B	protein_coding	protein_coding	ENST00000367412	12	28077

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.91e-10	0.976	125641	1	78	125720	0.000314

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.568	312	342	0.913	0.0000162	4303
Missense in Polyphen		122	129.68	0.94076		1549
Synonymous	0.379	114	119	0.956	0.00000605	1183
Loss of Function	2.24	20	34.1	0.587	0.00000143	502

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000559	0.000559
Ashkenazi Jewish	0.000107	0.0000992
East Asian	0.000272	0.000272
Finnish	0.0000464	0.0000462
European (Non-Finnish)	0.000239	0.000229
Middle Eastern	0.000272	0.000272
South Asian	0.000980	0.000948
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: The B chain of factor XIII is not catalytically active, but is thought to stabilize the A subunits and regulate the rate of transglutaminase formation by thrombin. {ECO:0000303|PubMed:21742792, ECO:0000303|PubMed:3021194}.
• Disease: DISEASE: Factor XIII subunit B deficiency (FA13BD) [MIM:613235]: An autosomal recessive hematologic disorder characterized by a life-long bleeding tendency, impaired wound healing and spontaneous abortion in affected women. {ECO:0000269|PubMed:11313256, ECO:0000269|PubMed:20331752, ECO:0000269|PubMed:26247044, ECO:0000269|PubMed:8324218}. 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;Blood Clotting Cascade;Androgen Receptor Network in Prostate Cancer;Dengue-2 Interactions with Complement and Coagulation Cascades;Dengue-2 Interactions with Blood Clotting Cascade;Steroid Biosynthesis;Complement and Coagulation Cascades;Hemostasis;Common Pathway of Fibrin Clot Formation;Formation of Fibrin Clot (Clotting Cascade) (Consensus)

Recessive Scores

• pRec: 0.258

Intolerance Scores

• loftool: 0.508
• rvis_EVS: 0.73
• rvis_percentile_EVS: 86.21

Haploinsufficiency Scores

• pHI: 0.128
• hipred: N
• hipred_score: 0.270

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.674

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: F13b
• Phenotype: homeostasis/metabolism phenotype

Gene ontology

• Biological process: blood coagulation;blood coagulation, fibrin clot formation;negative regulation of cellular protein catabolic process
• Cellular component: extracellular region