SERPINA7

serpin family A member 7, the group of Serpin peptidase inhibitors

Basic information

Region (hg38): X:106032434-106038727

Previous symbols: [ "TBG" ]

Links

ENSG00000123561 ∙ NCBI:6906 ∙ OMIM:314200 ∙ HGNC:11583 ∙ Uniprot:P05543 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Thyroxine-binding globulin deficiency; Thyroxine-binding globulin excess	XL	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Endocrine	8530630; 11600582; 11889160; 19415532

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SERPINA7 gene.

• not provided (13 variants)
• Inborn genetic diseases (10 variants)
• not specified (2 variants)
• Thyroxine-binding globulin quantitative trait locus (2 variants)
• Thyroxine-binding globulin deficiency (1 variants)
• Thyroxine-binding globulin, variant A (1 variants)
• Thyroxine-binding globulin, variant P (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SERPINA7 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					1	1
missense			13	2	4	19
nonsense						0
start loss						0
frameshift	1					1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	1	0	13	2	5

Variants in SERPINA7

This is a list of pathogenic ClinVar variants found in the SERPINA7 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-106033504-G-A			Likely benign (Feb 01, 2023)
X-106033506-T-G			Benign (Dec 31, 2019)
X-106033526-TCCCTAGAAAGAGAATACTC-T		Thyroxine-binding globulin quantitative trait locus	association (Oct 01, 2001)
X-106033545-C-A			Uncertain significance (Sep 02, 2022)
X-106033560-C-A			Uncertain significance (Jan 03, 2017)
X-106033585-T-C		not specified	Uncertain significance (Feb 06, 2024)
X-106033598-T-C		SERPINA7-related disorder • not specified	Conflicting classifications of pathogenicity (Aug 21, 2023)
X-106033600-G-A		Thyroxine-binding globulin quantitative trait locus	association (Feb 01, 1996)
X-106033633-AG-A		Thyroxine-binding globulin quantitative trait locus	association (Jun 01, 1996)
X-106033646-G-A			Uncertain significance (Oct 15, 2019)
X-106033675-C-T		not specified	Uncertain significance (Aug 08, 2022)
X-106033693-T-A			Benign (Feb 28, 2018)
X-106033697-G-A		Thyroxine-binding globulin deficiency, partial	association (Apr 01, 1991)
X-106033702-GC-G		Thyroxine-binding globulin quantitative trait locus	association (Oct 01, 2001)
X-106033711-G-A		SERPINA7-related disorder	Likely benign (Jul 03, 2019)
X-106034230-C-T		Thyroxine-binding globulin quantitative trait locus	association (Mar 01, 2002)
X-106034263-G-A		not specified	Uncertain significance (Oct 12, 2022)
X-106034293-T-A		Thyroxine-binding globulin, Chicago	Pathogenic (Nov 24, 1995)
X-106034369-AC-A		Thyroxine-binding globulin quantitative trait locus	association (Oct 01, 2001)
X-106034370-C-A		Thyroxine-binding globulin, variant P • not specified • Thyroxine-binding globulin quantitative trait locus • SERPINA7-related disorder	Benign (Feb 25, 2021)
X-106034380-C-T		Thyroxine-binding globulin quantitative trait locus	association (Feb 01, 1998)
X-106035127-C-T		not specified	Uncertain significance (May 27, 2022)
X-106035145-G-A		not specified	Uncertain significance (Jan 09, 2024)
X-106035202-AAG-A		Thyroxine-binding globulin quantitative trait locus	Pathogenic (Nov 18, 2019)
X-106035219-C-G		not specified	Uncertain significance (Feb 16, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SERPINA7	protein_coding	protein_coding	ENST00000327674	4	5533

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00261	0.803	125547	2	10	125559	0.0000478

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.656	166	144	1.15	0.00000978	2745
Missense in Polyphen		45	43.927	1.0244		970
Synonymous	-1.93	73	54.8	1.33	0.00000385	811
Loss of Function	1.06	5	8.28	0.604	5.24e-7	172

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000365	0.0000365
Ashkenazi Jewish	0.00	0.00
East Asian	0.000289	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.0000615	0.0000441
Middle Eastern	0.000289	0.000217
South Asian	0.000157	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Major thyroid hormone transport protein in serum.
• Pathway: Thyroid hormone synthesis - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.138

Intolerance Scores

• loftool: 0.119
• rvis_EVS: 0.99
• rvis_percentile_EVS: 90.56

Haploinsufficiency Scores

• pHI: 0.111
• hipred: N
• hipred_score: 0.131

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.162

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Serpina7

Gene ontology

• Biological process: negative regulation of endopeptidase activity;thyroid hormone transport
• Cellular component: extracellular region;extracellular space;extracellular exosome
• Molecular function: serine-type endopeptidase inhibitor activity