SERPINA12

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

Basic information

Region (hg38): 14:94487274-94517844

Links

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

Transcripts

Transcript IDs starting with ENST are treated as Ensembl, all others as RefSeq. Showing 4 of 8.

Transcript ID	Protein ID	Coding exons	MANE Select	MANE Plus Clinical
NM_001382267.1	NP_001369196.1	4	yes	-
ENST00000677451.1	ENSP00000503935.1	4	yes	-
NM_173850.4	NP_776249.1	4	-	-
NM_001304461.2	NP_001291390.1	4	-	-

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.

• not_specified (68 variants)
• not_provided (7 variants)
• Hereditary_palmoplantar_keratoderma,_Gamborg-Nielsen_type (2 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. These statistics are base on transcript: NM_001382267.1. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			1		2	3
missense			67	5	2	74
nonsense	1			1		2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	1	0	68	6	4

Highest pathogenic variant AF is 0.0000024787048

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
		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

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

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