SERPINA12

serpin family A member 12, the group of Serpin peptidase inhibitors

Basic information

Region (hg38): 14:94487273-94517844

Links

ENSG00000165953 ∙ NCBI:145264 ∙ OMIM:617471 ∙ HGNC:18359 ∙ Uniprot:Q8IW75 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• hereditary palmoplantar keratoderma, Gamborg-Nielsen type (Supportive), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SERPINA12 gene.

• Inborn genetic diseases (23 variants)
• not provided (6 variants)
• Hereditary palmoplantar keratoderma, Gamborg-Nielsen type (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SERPINA12 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					2	2
missense			22	2	2	26
nonsense				1		1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	3	4

Variants in SERPINA12

This is a list of pathogenic ClinVar variants found in the SERPINA12 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-94487327-C-A		not specified	Uncertain significance (May 24, 2023)
14-94487340-A-G		not specified	Uncertain significance (Sep 29, 2022)
14-94487427-T-C		not specified	Uncertain significance (Dec 07, 2023)
14-94487434-C-T		not specified	Uncertain significance (Aug 13, 2021)
14-94487481-G-T		not specified	Uncertain significance (Aug 23, 2021)
14-94487485-T-C		not specified	Uncertain significance (Feb 28, 2024)
14-94489622-C-A		Hereditary palmoplantar keratoderma, Gamborg-Nielsen type	Pathogenic (-)
14-94489639-C-T		not specified	Uncertain significance (Nov 17, 2022)
14-94489693-C-T			Likely benign (Mar 01, 2024)
14-94489721-C-T		not specified	Likely benign (May 26, 2023)
14-94489726-G-A		not specified	Uncertain significance (Jun 30, 2023)
14-94489739-G-A		not specified	Uncertain significance (Sep 22, 2023)
14-94489741-A-T		not specified	Uncertain significance (Nov 09, 2021)
14-94496377-G-A			Benign (Jul 23, 2018)
14-94496428-C-T		not specified	Uncertain significance (Nov 07, 2022)
14-94496455-G-A		not specified	Uncertain significance (Feb 16, 2023)
14-94496470-C-G		not specified	Uncertain significance (Jun 16, 2023)
14-94496476-T-C		not specified	Uncertain significance (Sep 16, 2021)
14-94496495-T-C			Benign (Jun 14, 2018)
14-94496502-A-G		not specified	Uncertain significance (Oct 06, 2021)
14-94496503-T-G		not specified	Uncertain significance (Dec 07, 2021)
14-94496528-G-A			Benign (Jun 14, 2018)
14-94496534-T-G		not specified	Uncertain significance (Mar 29, 2022)
14-94496560-T-C			Likely benign (Jul 23, 2018)
14-94496599-C-A		not specified	Uncertain significance (Jan 17, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SERPINA12	protein_coding	protein_coding	ENST00000341228	4	30571

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.72e-7	0.300	124288	5	1455	125748	0.00582

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.04	278	233	1.19	0.0000126	2757
Missense in Polyphen		88	70.607	1.2463		936
Synonymous	-0.453	103	97.3	1.06	0.00000611	796
Loss of Function	0.340	10	11.2	0.891	4.76e-7	149

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00512	0.00510
Ashkenazi Jewish	0.000211	0.000198
East Asian	0.00691	0.00693
Finnish	0.0120	0.0117
European (Non-Finnish)	0.00813	0.00791
Middle Eastern	0.00691	0.00693
South Asian	0.000823	0.000784
Other	0.00461	0.00441

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Adipokine that modulates insulin action by specifically inhibiting its target protease KLK7 in white adipose tissues. {ECO:0000269|PubMed:16030142}.

Recessive Scores

• pRec: 0.122

Intolerance Scores

• rvis_EVS: 1.42
• rvis_percentile_EVS: 94.92

Haploinsufficiency Scores

• pHI: 0.0333
• hipred: N
• hipred_score: 0.123
• ghis: 0.391

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.206

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Serpina12
• Phenotype: growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); homeostasis/metabolism phenotype; liver/biliary system phenotype

Gene ontology

• Biological process: negative regulation of endopeptidase activity;positive regulation of phosphatidylinositol 3-kinase signaling;negative regulation of gluconeogenesis;positive regulation of insulin receptor signaling pathway;negative regulation of lipid biosynthetic process;regulation of cholesterol metabolic process;regulation of triglyceride metabolic process
• Cellular component: extracellular space;plasma membrane
• Molecular function: serine-type endopeptidase inhibitor activity