PTCHD4

patched domain containing 4

Basic information

Region (hg38): 6:47856673-48111197

Previous symbols: [ "C6orf138" ]

Links

ENSG00000244694 ∙ NCBI:442213 ∙ OMIM:616908 ∙ HGNC:21345 ∙ Uniprot:Q6ZW05 ∙ 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 PTCHD4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PTCHD4 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		1
missense			46	1		47
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	46	2	0

Variants in PTCHD4

This is a list of pathogenic ClinVar variants found in the PTCHD4 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-47878326-G-A		not specified	Uncertain significance (May 13, 2024)
6-47878352-A-G		not specified	Uncertain significance (May 13, 2024)
6-47878374-T-C		not specified	Uncertain significance (Jul 14, 2021)
6-47878379-C-G		not specified	Uncertain significance (May 06, 2024)
6-47878389-T-C		not specified	Uncertain significance (Dec 12, 2023)
6-47878497-T-C		not specified	Uncertain significance (May 30, 2023)
6-47878595-C-T		not specified	Uncertain significance (Oct 25, 2023)
6-47878667-A-G		not specified	Uncertain significance (Feb 28, 2024)
6-47878668-T-G		not specified	Uncertain significance (Apr 12, 2024)
6-47878719-C-G		not specified	Uncertain significance (Jan 09, 2024)
6-47878733-G-A		not specified	Uncertain significance (Dec 21, 2022)
6-47878799-G-A		not specified	Uncertain significance (Nov 07, 2022)
6-47878845-C-T		not specified	Uncertain significance (Sep 13, 2023)
6-47878874-A-G		not specified	Uncertain significance (Jul 11, 2023)
6-47878891-G-T		not specified	Uncertain significance (Feb 17, 2024)
6-47878896-T-C		not specified	Uncertain significance (Aug 10, 2023)
6-47878997-C-T		not specified	Uncertain significance (May 15, 2024)
6-47879025-G-A		not specified	Uncertain significance (Apr 25, 2022)
6-47879078-C-T		not specified	Uncertain significance (Mar 31, 2024)
6-47879079-G-C		not specified	Uncertain significance (Feb 17, 2024)
6-47879124-C-T		not specified	Uncertain significance (Dec 06, 2022)
6-47879151-C-T		not specified	Uncertain significance (Jun 23, 2023)
6-47879223-G-A		not specified	Uncertain significance (Jan 29, 2024)
6-47879277-C-T		not specified	Likely benign (Aug 26, 2022)
6-47879444-A-G		not specified	Uncertain significance (Mar 11, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PTCHD4	protein_coding	protein_coding	ENST00000339488	3	190662

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000162	0.999	125565	0	28	125593	0.000111

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0727	468	464	1.01	0.0000239	5569
Missense in Polyphen		246	249.16	0.98731		3089
Synonymous	-1.64	224	195	1.15	0.0000105	1689
Loss of Function	2.82	11	26.7	0.412	0.00000151	307

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000338	0.000333
Ashkenazi Jewish	0.0000996	0.0000993
East Asian	0.000116	0.000109
Finnish	0.0000958	0.0000925
European (Non-Finnish)	0.0000903	0.0000881
Middle Eastern	0.000116	0.000109
South Asian	0.000196	0.000196
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Could act as a repressor of canonical hedgehog signaling by antagonizing the effects of SMO, as suggested by down- regulation of hedgehog target genes, including GLI1, PTCH1, and PTCH2 in PTCHD4-expressing cells. {ECO:0000269|PubMed:25296753}.

Intolerance Scores

• rvis_EVS: -0.71
• rvis_percentile_EVS: 14.71

Haploinsufficiency Scores

• pHI: 0.768
• hipred: N
• hipred_score: 0.393
• ghis: 0.413

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ptchd4

Gene ontology

• Biological process: biological_process
• Cellular component: cellular_component;integral component of membrane
• Molecular function: molecular_function