PDE6G

phosphodiesterase 6G, the group of Phosphodiesterases

Basic information

Region (hg38): 17:81650459-81663112

Previous symbols: [ "PDEG" ]

Links

ENSG00000185527 ∙ NCBI:5148 ∙ OMIM:180073 ∙ HGNC:8789 ∙ Uniprot:P18545 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• retinitis pigmentosa 57 (Definitive), mode of inheritance: AR
• retinitis pigmentosa 57 (Strong), mode of inheritance: AR
• retinitis pigmentosa (Supportive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Retinitis pigmentosa 57	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	Ophthalmologic	20655036

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PDE6G gene.

• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PDE6G 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	16		17
missense			36	2		38
nonsense	1		1			2
start loss			1			1
frameshift	1		2			3
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			3	3		6
non coding			11	12	9	32
Total	2	0	52	30	9

Highest pathogenic variant AF is 0.00000658

Variants in PDE6G

This is a list of pathogenic ClinVar variants found in the PDE6G region.

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

Position	Type	Phenotype	Significance	ClinVar
17-81650504-A-G		Retinitis pigmentosa	Benign (Jan 12, 2018)
17-81650511-A-G		Retinitis pigmentosa	Likely benign (Apr 27, 2017)
17-81650545-G-A		Retinitis pigmentosa	Uncertain significance (Mar 16, 2018)
17-81650548-G-A		Retinitis pigmentosa	Likely benign (Jan 12, 2018)
17-81650590-A-C		Retinitis pigmentosa	Benign (Jan 12, 2018)
17-81650654-C-T		Retinitis pigmentosa	Uncertain significance (Jan 13, 2018)
17-81650675-G-A		Retinitis pigmentosa	Benign (Jan 13, 2018)
17-81650681-G-A		Retinitis pigmentosa	Benign (Jan 13, 2018)
17-81650732-G-A		Retinitis pigmentosa	Uncertain significance (Jan 12, 2018)
17-81650758-C-T		Retinitis pigmentosa	Benign (Jan 12, 2018)
17-81650800-G-A		Retinitis pigmentosa	Benign (Jan 13, 2018)
17-81650841-A-G		Retinitis pigmentosa	Benign (Jan 13, 2018)
17-81650867-C-T		Retinitis pigmentosa	Uncertain significance (Mar 02, 2018)
17-81650906-TC-T		Retinitis Pigmentosa, Recessive	Likely benign (Jun 14, 2016)
17-81651029-C-T		Retinitis pigmentosa • Retinitis pigmentosa 57	Benign (Sep 05, 2021)
17-81651070-C-G		Retinitis pigmentosa	Uncertain significance (Jan 12, 2018)
17-81651070-C-T		Retinitis pigmentosa	Uncertain significance (Jan 13, 2018)
17-81651080-G-A			Likely benign (Oct 29, 2023)
17-81651082-T-A			Uncertain significance (Apr 03, 2022)
17-81651089-T-C			Likely benign (Jan 15, 2024)
17-81651090-T-C			Uncertain significance (Aug 12, 2022)
17-81651091-G-A			Uncertain significance (Feb 11, 2022)
17-81651093-G-A		not specified	Uncertain significance (Jun 13, 2023)
17-81651100-C-T			Uncertain significance (Oct 24, 2021)
17-81651101-G-A			Likely benign (Feb 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PDE6G	protein_coding	protein_coding	ENST00000331056	3	12654

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0134	0.682	124529	0	6	124535	0.0000241

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0272	50	49.5	1.01	0.00000250	561
Missense in Polyphen		23	25.157	0.91427		287
Synonymous	0.0351	19	19.2	0.990	9.92e-7	171
Loss of Function	0.571	3	4.27	0.702	1.83e-7	48

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000124	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000180	0.0000180
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Participates in processes of transmission and amplification of the visual signal. cGMP-PDEs are the effector molecules in G-protein-mediated phototransduction in vertebrate rods and cones.
• Disease: DISEASE: Retinitis pigmentosa 57 (RP57) [MIM:613582]: A retinal dystrophy belonging to the group of pigmentary retinopathies. Retinitis pigmentosa is characterized by retinal pigment deposits visible on fundus examination and primary loss of rod photoreceptor cells followed by secondary loss of cone photoreceptors. Patients typically have night vision blindness and loss of midperipheral visual field. As their condition progresses, they lose their far peripheral visual field and eventually central vision as well. {ECO:0000269|PubMed:20655036}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Purine metabolism - Homo sapiens (human);Phototransduction - Homo sapiens (human);Phosphodiesterases in neuronal function;Signaling by GPCR;Signaling by WNT;Signal Transduction;visual signal transduction;Purine nucleotides nucleosides metabolism;Ca2+ pathway;Beta-catenin independent WNT signaling;Visual signal transduction: Rods;G alpha (i) signalling events;Activation of the phototransduction cascade;Inactivation, recovery and regulation of the phototransduction cascade;The phototransduction cascade;Visual phototransduction;GPCR downstream signalling (Consensus)

Recessive Scores

• pRec: 0.134

Intolerance Scores

• loftool: 0.603
• rvis_EVS: 0.19
• rvis_percentile_EVS: 66.57

Haploinsufficiency Scores

• pHI: 0.207
• hipred: Y
• hipred_score: 0.517
• ghis: 0.470

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.867

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pde6g
• Phenotype: vision/eye phenotype; 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: activation of MAPK activity;visual perception;regulation of rhodopsin mediated signaling pathway;negative regulation of catalytic activity;positive regulation of epidermal growth factor receptor signaling pathway;positive regulation of G protein-coupled receptor signaling pathway;response to stimulus
• Cellular component: plasma membrane;photoreceptor disc membrane
• Molecular function: enzyme inhibitor activity;protein binding;spectrin binding;cGMP binding;3',5'-cyclic-GMP phosphodiesterase activity