PTCHD3

patched domain containing 3 (gene/pseudogene)

Basic information

Region (hg38): 10:27397121-27414368

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.

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. These statistics are base on transcript: . 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	6	5	78
nonsense				1		1
start loss						0
frameshift					1	1
splice donor/acceptor (+/-2bp)						0
Total	0	0	67	8	8

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