SERPINB7

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

Basic information

Region (hg38): 18:63752935-63805376

Links

ENSG00000166396 ∙ NCBI:8710 ∙ OMIM:603357 ∙ HGNC:13902 ∙ Uniprot:O75635 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• palmoplantar keratoderma, Nagashima type (Strong), mode of inheritance: AR
• palmoplantar keratoderma, Nagashima type (Supportive), mode of inheritance: AR
• palmoplantar keratoderma, Nagashima type (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Palmoplantar keratoderma, Nagashima type	AR	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	Dermatologic	24207119; 24773080

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SERPINB7 gene.

• Palmoplantar keratoderma, Nagashima type (4 variants)
• not provided (3 variants)
• SERPINB7-related disorder (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SERPINB7 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				6	2	8
missense			29	2	2	33
nonsense	2					2
start loss						0
frameshift	2	1				3
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2	1	3
non coding				2	12	14
Total	4	1	29	10	16

Highest pathogenic variant AF is 0.000322

Variants in SERPINB7

This is a list of pathogenic ClinVar variants found in the SERPINB7 region.

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

Position	Type	Phenotype	Significance	ClinVar
18-63782396-T-C		SERPINB7-related disorder	Likely benign (May 23, 2019)
18-63782420-CAG-C		SERPINB7-related disorder	Likely pathogenic (Jan 04, 2024)
18-63782480-C-T			Likely benign (Jun 01, 2023)
18-63782493-C-G		Inborn genetic diseases	Uncertain significance (May 09, 2022)
18-63782504-G-A			Likely benign (Sep 20, 2023)
18-63782529-C-T		Palmoplantar keratoderma, Nagashima type	Pathogenic (Feb 21, 2020)
18-63782540-G-T			Uncertain significance (Jun 24, 2021)
18-63792132-G-A			Benign (Nov 12, 2018)
18-63792182-A-G			Benign (Nov 12, 2018)
18-63792385-G-C			Likely benign (Aug 04, 2023)
18-63792405-A-G		SERPINB7-related disorder	Benign (Nov 27, 2023)
18-63792409-C-G		Inborn genetic diseases	Uncertain significance (Feb 17, 2024)
18-63792429-T-C		Inborn genetic diseases	Uncertain significance (Aug 30, 2021)
18-63792437-T-A			Uncertain significance (Mar 24, 2023)
18-63792442-AG-TAAACTTTACCT		Palmoplantar keratoderma, Nagashima type	Pathogenic (Oct 01, 2014)
18-63792836-G-A			Benign (Nov 12, 2018)
18-63793052-A-T			Benign (Nov 12, 2018)
18-63793161-T-C		Inborn genetic diseases	Conflicting classifications of pathogenicity (Oct 03, 2022)
18-63793164-G-A		Inborn genetic diseases	Uncertain significance (Jan 29, 2024)
18-63793242-G-A		Inborn genetic diseases	Uncertain significance (Apr 15, 2024)
18-63793251-G-C		Inborn genetic diseases	Uncertain significance (Mar 27, 2023)
18-63796247-A-G			Benign (Jul 23, 2022)
18-63796289-A-G			Likely benign (Jul 21, 2023)
18-63796295-C-T			Likely benign (Nov 08, 2022)
18-63796318-A-T		Inborn genetic diseases	Uncertain significance (Aug 08, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SERPINB7	protein_coding	protein_coding	ENST00000398019	7	52436

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.38e-9	0.271	125497	0	250	125747	0.000995

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.532	225	204	1.10	0.0000104	2515
Missense in Polyphen		78	72.055	1.0825		914
Synonymous	-0.248	82	79.2	1.04	0.00000443	707
Loss of Function	0.613	14	16.7	0.838	8.69e-7	208

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000192	0.000185
Ashkenazi Jewish	0.00	0.00
East Asian	0.0109	0.0107
Finnish	0.00	0.00
European (Non-Finnish)	0.000363	0.000360
Middle Eastern	0.0109	0.0107
South Asian	0.000345	0.000327
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Might function as an inhibitor of Lys-specific proteases. Might influence the maturation of megakaryocytes via its action as a serpin.

Recessive Scores

• pRec: 0.145

Intolerance Scores

• loftool: 0.276
• rvis_EVS: -0.36
• rvis_percentile_EVS: 29.16

Haploinsufficiency Scores

• pHI: 0.249
• hipred: N
• hipred_score: 0.146
• ghis: 0.547

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.450

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Serpinb7

Gene ontology

• Biological process: negative regulation of endopeptidase activity;positive regulation of transforming growth factor beta1 production;positive regulation of collagen biosynthetic process;positive regulation of glomerular mesangial cell proliferation;positive regulation of platelet-derived growth factor production
• Cellular component: extracellular space;cytoplasm
• Molecular function: serine-type endopeptidase inhibitor activity