PTCHD1

patched domain containing 1

Basic information

Region (hg38): X:23334848-23404374

Links

ENSG00000165186 ∙ NCBI:139411 ∙ OMIM:300828 ∙ HGNC:26392 ∙ Uniprot:Q96NR3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• autism, susceptibility to, X-linked 4 (Definitive), mode of inheritance: XLR
• autism, susceptibility to, X-linked 4 (Strong), mode of inheritance: XL
• autism, susceptibility to, X-linked 4 (Definitive), mode of inheritance: XL
• autism, susceptibility to, X-linked 4 (Definitive), mode of inheritance: XL
• non-syndromic X-linked intellectual disability (Definitive), mode of inheritance: XL

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Autism susceptibility, X-linked 4	XL	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	Neurologic	18252227; 21091464; 25131214

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PTCHD1 gene.

• not provided (111 variants)
• Inborn genetic diseases (58 variants)
• not specified (21 variants)
• Autism, susceptibility to, X-linked 4 (17 variants)
• PTCHD1-related condition (4 variants)
• Intellectual disability (1 variants)
• Abnormal brain morphology (1 variants)
• PTCHD1-related autism and intellectual disability (1 variants)
• Developmental disorder (1 variants)
• Neurodevelopmental disorder (1 variants)
• PTCHD1-related neurodevelopmental disorder (1 variants)
• See cases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PTCHD1 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			5	24	3	32
missense		2	92	3	2	99
nonsense		7		1		8
start loss		1				1
frameshift	4	6	1			11
inframe indel			4			4
splice donor/acceptor (+/-2bp)			1			1
splice region				1		1
non coding				3	10	13
Total	4	16	103	31	15

Variants in PTCHD1

This is a list of pathogenic ClinVar variants found in the PTCHD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-23334877-T-C			Likely pathogenic (Feb 25, 2021)
X-23334891-C-T		not specified	Uncertain significance (Sep 11, 2017)
X-23334893-G-A			Likely benign (Feb 06, 2020)
X-23334902-C-T		Inborn genetic diseases	Likely benign (Jan 10, 2018)
X-23334922-G-A		Autism, susceptibility to, X-linked 4	Uncertain significance (Jul 23, 2018)
X-23334924-C-G		Inborn genetic diseases	Uncertain significance (Jan 22, 2024)
X-23334946-A-C			Uncertain significance (Oct 22, 2021)
X-23334951-GTCT-G		Inborn genetic diseases	Uncertain significance (Jan 12, 2022)
X-23334953-C-T		Inborn genetic diseases	Likely benign (Dec 03, 2018)
X-23334968-G-A		not specified • Inborn genetic diseases	Benign (Sep 27, 2018)
X-23334970-C-G		Intellectual disability	Likely pathogenic (Apr 06, 2021)
X-23334970-C-T		Autism, susceptibility to, X-linked 4	Uncertain significance (Apr 12, 2016)
X-23334980-C-G		Inborn genetic diseases	Uncertain significance (Oct 20, 2023)
X-23334988-T-A		Autism, susceptibility to, X-linked 4	Uncertain significance (Dec 29, 2016)
X-23334990-C-T		Inborn genetic diseases • Autism, susceptibility to, X-linked 4	Uncertain significance (Feb 24, 2022)
X-23334991-T-A			Uncertain significance (Apr 27, 2022)
X-23334992-C-G			Likely benign (Oct 17, 2017)
X-23334992-C-T		Inborn genetic diseases	Likely benign (Feb 11, 2019)
X-23335018-T-C		Inborn genetic diseases	Uncertain significance (Aug 02, 2023)
X-23335019-CGAG-C		Autism, susceptibility to, X-linked 4	Uncertain significance (Nov 28, 2022)
X-23335020-G-A		See cases	Uncertain significance (Jan 13, 2022)
X-23335038-C-T		Inborn genetic diseases	Likely benign (Apr 13, 2017)
X-23335042-T-G			Uncertain significance (Sep 29, 2022)
X-23335045-C-A			Uncertain significance (Feb 02, 2023)
X-23335054-A-G			Uncertain significance (Feb 24, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PTCHD1	protein_coding	protein_coding	ENST00000379361	3	70357

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.982	0.0178	125350	0	1	125351	0.00000399

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.00	238	342	0.695	0.0000258	5849
Missense in Polyphen		69	135.04	0.51096		2434
Synonymous	-0.225	148	145	1.02	0.0000114	1794
Loss of Function	3.56	1	16.7	0.0599	0.00000112	336

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	0.0000524	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for the development and function of the thalamic reticular nucleus (TRN), a part of the thalamus that is critical for thalamocortical transmission, generation of sleep rhythms, sensorimotor processing and attention. {ECO:0000250|UniProtKB:Q14B62}.

Recessive Scores

• pRec: 0.114

Intolerance Scores

• loftool: 0.0945
• rvis_EVS: -1
• rvis_percentile_EVS: 8.32

Haploinsufficiency Scores

• pHI: 0.532
• hipred: Y
• hipred_score: 0.768
• ghis: 0.625

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.238

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ptchd1
• Phenotype: growth/size/body region phenotype; muscle phenotype; immune system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); hematopoietic system 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); hearing/vestibular/ear phenotype

Gene ontology

• Biological process: smoothened signaling pathway;thalamus development;social behavior;cognition
• Cellular component: plasma membrane;integral component of membrane
• Molecular function: molecular_function