PRSS12

serine protease 12, the group of Scavenger receptor cysteine rich domain containing|Serine proteases

Basic information

Region (hg38): 4:118280037-118353003

Links

ENSG00000164099 ∙ NCBI:8492 ∙ OMIM:606709 ∙ HGNC:9477 ∙ Uniprot:P56730 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• intellectual disability, autosomal recessive 1 (Definitive), mode of inheritance: AR
• autosomal recessive non-syndromic intellectual disability (Supportive), mode of inheritance: AR
• non-syndromic intellectual disability (Limited), mode of inheritance: AR
• intellectual disability, autosomal recessive 1 (Limited), mode of inheritance: Unknown
• non-syndromic intellectual disability (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Intellectual developmental disorder, autosomal recessive 1	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	Neurologic	12459588; 12925575

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PRSS12 gene.

• Intellectual disability, autosomal recessive 1 (111 variants)
• not specified (46 variants)
• Inborn genetic diseases (44 variants)
• not provided (27 variants)
• Intellectual Disability, Recessive (8 variants)
• Intellectual disability (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRSS12 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			11	15	5	31
missense			86	8	1	95
nonsense		1	7			8
start loss						0
frameshift			3			3
inframe indel						0
splice donor/acceptor (+/-2bp)			4			4
splice region			2	1		3
non coding			37	8	4	49
Total	0	1	148	31	10

Variants in PRSS12

This is a list of pathogenic ClinVar variants found in the PRSS12 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-118280071-A-G		Intellectual disability, autosomal recessive 1	Likely benign (Jan 13, 2018)
4-118280237-A-G		Intellectual disability, autosomal recessive 1	Uncertain significance (Jan 13, 2018)
4-118280276-A-G		Intellectual disability, autosomal recessive 1	Uncertain significance (Jan 12, 2018)
4-118280321-G-A		Intellectual disability, autosomal recessive 1	Uncertain significance (Jan 13, 2018)
4-118280341-T-C		Intellectual disability, autosomal recessive 1	Benign (Apr 27, 2017)
4-118280359-T-C		Intellectual disability, autosomal recessive 1	Uncertain significance (Jan 13, 2018)
4-118280363-C-T		Intellectual disability, autosomal recessive 1	Uncertain significance (Jan 12, 2018)
4-118280376-GTT-G		Intellectual Disability, Recessive	Benign (Jun 14, 2016)
4-118280432-C-T		Intellectual disability, autosomal recessive 1	Likely benign (Apr 27, 2017)
4-118280437-T-C		Intellectual disability, autosomal recessive 1	Uncertain significance (Jan 13, 2018)
4-118280501-T-C		Intellectual disability, autosomal recessive 1	Uncertain significance (Jan 12, 2018)
4-118280505-G-A		Intellectual disability, autosomal recessive 1	Uncertain significance (Jan 13, 2018)
4-118280793-G-A		Intellectual disability, autosomal recessive 1	Uncertain significance (Jan 12, 2018)
4-118280795-A-G		Intellectual disability, autosomal recessive 1	Uncertain significance (Apr 27, 2017)
4-118280986-T-G		Intellectual disability, autosomal recessive 1	Uncertain significance (Jan 13, 2018)
4-118281016-C-G		Intellectual disability, autosomal recessive 1	Uncertain significance (Jan 13, 2018)
4-118281024-C-T		Intellectual disability, autosomal recessive 1	Benign (Apr 27, 2017)
4-118281030-T-C		Intellectual disability, autosomal recessive 1	Uncertain significance (Jan 12, 2018)
4-118281032-T-A		Intellectual disability, autosomal recessive 1	Uncertain significance (Jan 13, 2018)
4-118281087-G-A		Intellectual disability, autosomal recessive 1	Uncertain significance (Jan 13, 2018)
4-118281094-G-C		Intellectual disability, autosomal recessive 1	Uncertain significance (Jan 12, 2018)
4-118281097-A-G		Intellectual disability, autosomal recessive 1	Uncertain significance (Jan 12, 2018)
4-118281106-G-A		Intellectual disability, autosomal recessive 1	Uncertain significance (Jan 13, 2018)
4-118281129-C-T		Intellectual disability, autosomal recessive 1	Likely benign (Apr 27, 2017)
4-118281136-C-T		Intellectual disability, autosomal recessive 1	Uncertain significance (Feb 02, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PRSS12	protein_coding	protein_coding	ENST00000296498	13	72966

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.38e-29	0.000190	125006	2	740	125748	0.00295

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.387	460	484	0.951	0.0000260	5628
Missense in Polyphen		165	175.14	0.94208		2074
Synonymous	0.402	175	182	0.962	0.00000952	1727
Loss of Function	0.221	44	45.6	0.965	0.00000249	503

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00357	0.00357
Ashkenazi Jewish	0.00258	0.00258
East Asian	0.00235	0.00234
Finnish	0.00989	0.00984
European (Non-Finnish)	0.00178	0.00173
Middle Eastern	0.00235	0.00234
South Asian	0.00503	0.00498
Other	0.00163	0.00163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in neuronal plasticity and the proteolytic action may subserve structural reorganizations associated with learning and memory operations. {ECO:0000250}.

Recessive Scores

• pRec: 0.136

Intolerance Scores

• loftool: 0.310
• rvis_EVS: 0.07
• rvis_percentile_EVS: 59.16

Haploinsufficiency Scores

• pHI: 0.206
• hipred: N
• hipred_score: 0.361
• ghis: 0.395

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.247

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Prss12
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Gene ontology

• Biological process: exocytosis;receptor-mediated endocytosis;zymogen activation
• Cellular component: plasma membrane;axon;dendrite;cytoplasmic vesicle;synaptic cleft;terminal bouton
• Molecular function: serine-type endopeptidase activity;scavenger receptor activity;serine-type peptidase activity