PTCHD3

patched domain containing 3 (gene/pseudogene)

Basic information

Region (hg38): 10:27397120-27414368

Links

ENSG00000182077 ∙ NCBI:374308 ∙ OMIM:611791 ∙ HGNC:24776 ∙ Uniprot:Q3KNS1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PTCHD3 gene.

• Inborn genetic diseases (45 variants)
• not provided (11 variants)
• not specified (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PTCHD3 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	2	3
missense			41	4	5	50
nonsense				1		1
start loss						0
frameshift					1	1
inframe indel				1		1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	41	7	8

Variants in PTCHD3

This is a list of pathogenic ClinVar variants found in the PTCHD3 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-27398431-G-A		not specified	Uncertain significance (Oct 04, 2022)
10-27398452-T-C		not specified	Uncertain significance (Nov 30, 2022)
10-27398499-G-A		not specified	Uncertain significance (Apr 13, 2022)
10-27398508-C-A		not specified	Uncertain significance (Aug 16, 2021)
10-27398625-A-G		not specified	Uncertain significance (Jan 05, 2022)
10-27398657-C-G		not specified	Uncertain significance (Jan 26, 2023)
10-27398709-C-A		not specified	Uncertain significance (Dec 19, 2022)
10-27398745-T-C		not specified	Uncertain significance (Oct 06, 2022)
10-27398985-A-G		not specified	Uncertain significance (Mar 28, 2023)
10-27399007-T-C		not specified	Uncertain significance (Apr 07, 2022)
10-27399042-G-T		not specified	Uncertain significance (May 17, 2023)
10-27399124-T-C		not specified	Uncertain significance (Dec 07, 2021)
10-27399129-A-G		not specified	Uncertain significance (Dec 06, 2021)
10-27399141-G-A		not specified	Likely benign (Dec 20, 2023)
10-27399160-A-G		not specified	Uncertain significance (Feb 07, 2023)
10-27399162-A-G		not specified	Uncertain significance (Jan 04, 2024)
10-27399171-C-T		not specified	Uncertain significance (Jan 18, 2022)
10-27399172-G-A			Likely benign (Mar 01, 2022)
10-27399226-C-A		not specified	Uncertain significance (Jan 24, 2024)
10-27399240-C-T		not specified	Uncertain significance (Jun 11, 2021)
10-27399244-T-TAAAAA			Likely benign (Dec 30, 2023)
10-27399255-AAAAAG-A			Likely benign (Dec 30, 2023)
10-27403241-A-G		not specified	Uncertain significance (Sep 27, 2021)
10-27403317-C-T		not specified	Uncertain significance (Jul 06, 2021)
10-27403327-A-G			Likely benign (Aug 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PTCHD3	protein_coding	protein_coding	ENST00000438700	4	16182

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.33e-10	0.306	58078	12613	55052	125743	0.320

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.360	468	447	1.05	0.0000267	4991
Missense in Polyphen		107	98.865	1.0823		1220
Synonymous	-0.660	214	202	1.06	0.0000145	1524
Loss of Function	0.867	17	21.3	0.797	0.00000101	255

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.546	0.548
Ashkenazi Jewish	0.374	0.372
East Asian	0.165	0.165
Finnish	0.303	0.297
European (Non-Finnish)	0.379	0.375
Middle Eastern	0.165	0.165
South Asian	0.329	0.327
Other	0.337	0.333

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in sperm development or sperm function. {ECO:0000269|PubMed:17904097}.

Recessive Scores

• pRec: 0.120

Intolerance Scores

• loftool: 0.153
• rvis_EVS: 3.16
• rvis_percentile_EVS: 99.31

Haploinsufficiency Scores

• pHI: 0.0816
• hipred: N
• hipred_score: 0.123
• ghis: 0.387

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0393

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ptchd3

Gene ontology

• Biological process: spermatid development
• Cellular component: cellular_component;integral component of membrane;sperm midpiece
• Molecular function: molecular_function