PRR12

proline rich 12

Basic information

Region (hg38): 19:49591182-49626439

Previous symbols: [ "KIAA1205" ]

Links

ENSG00000126464 ∙ NCBI:57479 ∙ OMIM:616633 ∙ HGNC:29217 ∙ Uniprot:Q9ULL5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• neuroocular syndrome (Strong), mode of inheritance: AD
• neuroocular syndrome (Definitive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Neuroocular syndrome 1	AD	Cardiovascular; Renal	The condition can include congenital anomalies such as cardiac and renal anomalies, and awareness may allow early interventions (eg, surgical repair of cardiac anomalies)	Cardiovascular; Craniofacial; Musculoskeletal; Neurologic; Ophthalmologic; Renal	29556724; 33314030; 33824499

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PRR12 gene.

• not provided (17 variants)
• Neuroocular syndrome (10 variants)
• Neuroocular syndrome 1 (3 variants)
• Inborn genetic diseases (3 variants)
• Motor delay;Abnormality of vision;Iris coloboma;Autism;Delayed speech and language development (1 variants)
• Intellectual disability (1 variants)
• Motor delay;Abnormality of vision;Delayed speech and language development;Iris coloboma;Autism (1 variants)
• Motor delay;Autism;Abnormality of vision;Delayed speech and language development;Iris coloboma (1 variants)
• Neurodevelopmental disorder (1 variants)
• PRR12-related disorder (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRR12 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	62	29	92
missense		1	172	75	5	253
nonsense	10	5				15
start loss						0
frameshift	20	8	1			29
inframe indel			7	1		8
splice donor/acceptor (+/-2bp)						0
splice region			3	1	2	6
non coding				1	1	2
Total	30	14	181	139	35

Variants in PRR12

This is a list of pathogenic ClinVar variants found in the PRR12 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-49591652-T-G		PRR12-related disorder	Likely benign (Jun 12, 2019)
19-49591719-A-G		Inborn genetic diseases	Uncertain significance (Oct 26, 2022)
19-49591728-C-A			Likely pathogenic (Jun 25, 2024)
19-49593326-G-T			Pathogenic (Nov 01, 2024)
19-49593423-C-T			Likely benign (Jun 01, 2024)
19-49593433-C-T			Uncertain significance (Apr 22, 2024)
19-49594459-T-A		Inborn genetic diseases	Uncertain significance (Jun 24, 2022)
19-49594474-A-C		Inborn genetic diseases	Likely benign (Oct 01, 2023)
19-49594489-G-A		PRR12-related disorder	Benign (Dec 31, 2019)
19-49594490-C-A		Inborn genetic diseases	Uncertain significance (Apr 29, 2020)
19-49594515-C-T		PRR12-related disorder	Likely benign (Mar 27, 2019)
19-49594527-T-C		PRR12-related disorder	Benign (Oct 21, 2019)
19-49594547-G-T		Inborn genetic diseases	Uncertain significance (Nov 07, 2022)
19-49594553-C-A		Inborn genetic diseases	Uncertain significance (Mar 12, 2024)
19-49594567-T-C			Uncertain significance (Jun 15, 2022)
19-49594569-C-T		PRR12-related disorder	Benign (Oct 27, 2021)
19-49594571-C-T			Uncertain significance (Mar 07, 2022)
19-49594585-T-TC			Pathogenic (Jan 06, 2021)
19-49594596-C-T			Likely benign (Mar 01, 2024)
19-49594613-C-T			Uncertain significance (Oct 12, 2023)
19-49594719-G-A		PRR12-related disorder	Likely benign (Jun 22, 2021)
19-49594724-T-C		Inborn genetic diseases	Uncertain significance (Sep 10, 2024)
19-49594758-C-T		PRR12-related disorder	Likely benign (Dec 31, 2021)
19-49594815-C-T			Benign (Dec 31, 2019)
19-49594822-C-T		Inborn genetic diseases	Uncertain significance (May 09, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PRR12	protein_coding	protein_coding	ENST00000418929	14	34797

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	7.66e-10	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.98	970	1.27e+3	0.765	0.0000859	12597
Missense in Polyphen		120	201.01	0.597		1845
Synonymous	-3.29	689	588	1.17	0.0000443	4644
Loss of Function	7.04	0	57.7	0.00	0.00000284	700

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.114

Haploinsufficiency Scores

• pHI: 0.391
• hipred: Y
• hipred_score: 0.675
• ghis: 0.525

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.186

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Prr12

Gene ontology

• Cellular component: nucleus;postsynaptic density;cell junction;neuron projection;postsynaptic membrane