PTCHD1-AS

PTCHD1 antisense RNA (head to head), the group of Antisense RNAs

Basic information

Region (hg38): X:22162728-23333685

Links

ENSG00000233067 ∙ NCBI:100873065 ∙ ∙ HGNC:37703 ∙ ∙ ∙ 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 PTCHD1-AS gene.

• not provided (218 variants)
• Familial X-linked hypophosphatemic vitamin D refractory rickets (77 variants)
• Hypophosphatemic rickets (8 variants)
• not specified (3 variants)
• Inborn genetic diseases (2 variants)
• See cases (1 variants)
• Vitamin D-dependent rickets, type 2 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PTCHD1-AS 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						0
missense						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)	1			1		2
splice region						0
non coding	137	51	34	17	24	263
Total	138	51	34	18	24

Variants in PTCHD1-AS

This is a list of pathogenic ClinVar variants found in the PTCHD1-AS 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-22164572-TTCACCAGCATGCTCTGGAAAGACCAGTCTTCAGAAAACAATTGTGGATGACTCAGCTTGTCCGTTCGTTCGTTCTTTTCTTTTCTTCTTTTCTTTTCTCTCTCTCTCTTTTTCTCACTTTCTCTCCAAAACTATCTGGAATTCTTTACTTGCTATAGTTATGCATATGACTTATAGCGAGCTGATAAAATATAGTGCAAAATTAAATACAATGCCGGAAATAATAGAATAATCTCAGAATGAGGTAACCTATAGATGTATGACATAGTTTGGTGTTGGGGGTAGAGTTGTAACCTCTAGTTATCTGCTATCTGGGTCACATCAAGCTTTTAGTGTGTGTAACTCACAGAGTTTTGAAGGTGTAATTTGATCTGTGCTATACTTGAGTCTGTGAAACAGCAAAACCCATTATGACTATGTCCTACAGCCCTTGTAAAATCCTAAGTCTTGAGCTTCAGGATTCTGCTGATATTTAATATCTGAATTATTTCAAGGAAGGTAAGGAAAGTGTACTATCTTACTATGTTTATTTCTTGAGTGAGGAAAATTGAAAGGGACTAAAGGAAAGAACTCGTTGCCAAGAGCAGTGTCCAGAGGTCACTGGTTTTGCTTTGTGGCTTTGCTGGAATAAAACCAACGTGTTTGGGGTTGCCTAGGTCTTATGTTGGGTCATCTGGAGGCAGATCTGGAGATGAGAATTCCTGTGTAAGTGATTCATTAAACAAATACTCCCAAGAGAAATCAGTAAGGGAATGGGAGAAGCAAGACAGGGAGGGATGAGAGTCCAATTTCAGGAGACATCTCAGAACTAGTCTGATCCTGCAGGGAACTTTGGAAGTACAAATTATACCTCAGAGTTTGTCCTGAATTGAGGCAAGGGGGCTGGGCTTTCATATTGCCGCTTAGGGCTGCTTGGGTGGAGGCAGAGGCGGAGGCGGAGGTGCAGGTGCAGGAAAAGTGGGTAGAAGGCAAATAAACCCCCAGGAACTAGCTATTTTTGATTGCAGGCAAGGAGCTCTAGTAGTTCCTAGGGCAGGCCTTCAGAAAGTCTCAGGTGTTGGCCATTAGAAAAGAAAAAACATAGATGCTGGAGGGATGTACAGAAGTTATAAAAGGGATCCCAGGGAATCTGGTCAGAGCCCTGACAGTGTACTTGTAAGCTTCTCTTTTGCTTTTATGAAACCCAGAATCTGGAGAAGGGAGAGAGAAATTTTCACATGGAACTGTAAAGTTTCTCTAAAGCAAGGGTTGACGAACTTTTTCTAGAAAGGGCCAGATAAAATATTTGAGGCTTTGTGGGCCACAGGGTGTCTGACCCAATTATTCAACTCTACAACTGTACTGCAGAAGCAGCCATAGTTGACAGGTAAACAAATGAGTGTGGCTATGTTCCAATAAAACTTTATTTATAAAAACAGGGGTAGGGTGGCTGGATTTGGCCCAGGGACCATATTTTGCCAATCGCTGCTCTTGAGGTTCTTTATATGTGCCTAAGTTTGTTTTTCCTTTATTTATTCCCTATCTGTTATAAAACACAGAGGATAATTAGTACCTTTGTCTATCTAAATGATGGTTATGACATTATGATGTATCTTAAATTATTCTAGATCACTGCCTCCAATCTTTCTGGCATCCTGGCCATCTTTCACAATGTTGCAAAGATAATCTTCCTGAAGCATGACTCATCTCCTTTTATTCCCATGCTAAACATATTTAGCTCTCTCTTAGCTGTAAAATAAAATATAGGCTTGTTAACATGGCATTCAGGAATCCCTGTGATCTGACCCCAGGCCAATTTTCCTGCATTATTTTCTGTTCTCCATCCTCATGTACTTATAGTCCAGCTACATTAAATTACTCGCCCTCTCTCCAATATGCCATATCGTGTGTGTTTGCTATCTCCTTGTAGTTTTTTTCATTTTTATGTATTTAAACTGACTATATACTGTCAAAATTTTATATATATATATATGATGTACAACATGATGTTTTGATACATGTATACATTAGAAAATGGGTAAATTAACATATCCATCACCTCATATATTTATCATTTTTGTGGTAAGAACATTTAAAATCTACTCCCTTAGCCATTTTCTAGTGTACAATACATTGATATTAACTATAGTCACTATGTTGTACAATACATCTCCTAAACTTATTCCTCTTATCTAACTGAAATTTTGTATCTTTTGACCAACTCCCTAACCCCATTCCCCCACCCCTGGTAACCACCATCCTACTGTACTCTGTTATGAGTTTGACTGCTTTAAATTTCGCATGAATGAGATCATGCAGTATTTGCCTTTTGGTGCCTGGCTTATTTCACTTAGCATGAAGTCCTACAGATTCATCCACGTTGTCACAAATGACAGGATTTTCTTCTTTTTTAAAGCTGAATAGTATTCCATTGTGTATATATACTACATTTTATATTCCATTGTGTACATATACTACATTTTTAATCCATTCCTCTGTTAATAGACATTTAGGTTAATTCCATATCTTGGCTATTTTGAATAGTGCTTCAATGAACATGGAGGCACTCTCTTTAGCGTACTGATTTCATTTCCTTTGGATATATCCCCAGAAGTAGGATTACTGCTTTGTATGGTAGTTACATTTTTAATTTTTAGAGGAACCTCCATAGTGTTTTTCATAGTGACTGTACCAAATTATATTGCCACCAACAGTGCTCAAGAGTTCCCTTTTCTCCACACCCTTACCAACACTTGTTATCTCTTGTCTTGTTGATAGTCGCCATTCTAACTGGTGATAGGTAATATCTCATTGTGTTTTTAATTTTTATTTCCCTGATGAGTAATGATGTGGATCATTAAAAAAATCTGTTGACAATTTGCATGTCTTCTTTTGAGAAATGTATTTTCACGTTATTTTCCCTTTTTAATTTTTTAATTTCTTTTTTTTTTTTTTTTTGGAGACAGGGTCTTGTTCTGTCACCCAGGCTGGAGTGCAGTAGTGTGATCATAGTTCACTGCAGCCTCTACCTCCCAGGCTCAAGTGATCCTCCTGCCTCAACCTCCCAAGTAATTGGAACTATAGGCAGGTGCCACCATGCCCGGCTTTTTTTAAAATTTATTTTTGTAGAGACAGGGTCCCGCTGTGTTGCCCAGGCTGGTCTTGAATTCCTGGCCTCAAGCAATCCTCCTGCCTCAGCCTCCCAAAGCTCTGGGATTACAGGCATGAACAACTGTGCCCGACCTCCTTTCCCCATTTTTTAACCAGGTGATTTGCTTTCTTGATATTGAGTTGAGTTTTAAATATATTTTGGATATTAACCCTTTATCAGATGTATGGTTTGCACATATTTTTGCCTCTGTCTTTGCCCCTGTTTCTTCTCCTGGAATGTTCTTCTAGCTCTACATTTTGAAATCCTAACCATTCTCTTAAGACTCGATTCAGTCACCTTCTCCATTAAGCATTTTCTCCATGCAGAAACAGTCTCTCCTCTGGACTTTGATAACAATATTGTCTATTTCTATTAAATTTTTTATTTTGTTTACATTGTACTAGACAGTTATTTGCTACATTCACTGCATTTTTAGTATACTGAGGTCTCTCAATATATATCTATATATTTTTGCCCTTCACAGTGGCTTGCATATAGTAGATATTCAGTAAATGGAGTTTTCAGATGAAGGGCGCATTTCTACATCTTGTGATTATTAATGATTTAAGTGCTGAAACTCTGACATTATTTTTCTTTTTCCTTTTTGTAGGCGAGAGCTGTTTTGGCAAAAGTTGGCTATCCAGAGTTTATAATGAATGATACTC-T			Likely pathogenic (Aug 02, 2019)
X-22168306-TTGTAGGCGAGAGC-T			Likely pathogenic (Mar 04, 2022)
X-22168307-TG-T		PHEX-related disorder	Benign (Dec 17, 2021)
X-22168313-C-A		Familial X-linked hypophosphatemic vitamin D refractory rickets	Pathogenic/Likely pathogenic (Mar 17, 2022)
X-22168313-C-T		Inborn genetic diseases	Conflicting classifications of pathogenicity (Nov 25, 2023)
X-22168318-GCTGTTT-G			Pathogenic (Jul 14, 2023)
X-22168322-T-A			Likely pathogenic (Nov 04, 2022)
X-22168328-CA-C		Familial X-linked hypophosphatemic vitamin D refractory rickets	Pathogenic (May 28, 2019)
X-22168333-G-A		Familial X-linked hypophosphatemic vitamin D refractory rickets	Uncertain significance (Dec 17, 2021)
X-22168341-T-A			Pathogenic (Nov 05, 2018)
X-22168341-T-C			Likely benign (Feb 17, 2021)
X-22168344-A-G		Familial X-linked hypophosphatemic vitamin D refractory rickets	Benign/Likely benign (Aug 24, 2023)
X-22168350-TATAATGA-T			Pathogenic (Oct 09, 2020)
X-22168350-TATAATGAATGATACTCATGTTAATGAAGACCTCAAAGCTGTAAGTGCTAAATTTACTGTACTTTTTTTTTTCTGGCAAGTTTTACTGGCCTTGTGCCTTTCAACTAACCCAAGTCCTAGCAATTAAAACTGGTGATGCCAGAAAACACCAACTTTTGATTAATTCCTTGGCTAGATATGAGCCTGAATATGCCAGGCAGATCACAAGATTTAGGGCAGATTCAAAATAAAGAAGTGTCAGAAACGATGCGTAGCTGAGTGGGTACCAAAAAAC-T			Likely pathogenic (Jan 22, 2022)
X-22168355-T-C		Inborn genetic diseases	Uncertain significance (Jun 12, 2023)
X-22168361-A-G			Uncertain significance (Mar 04, 2022)
X-22168367-AT-A			Pathogenic (Jun 09, 2023)
X-22168368-T-C		not specified	Benign/Likely benign (Sep 08, 2023)
X-22168377-A-T			Likely benign (Apr 21, 2022)
X-22168379-AC-A		Familial X-linked hypophosphatemic vitamin D refractory rickets	Likely pathogenic (Dec 20, 2022)
X-22168383-CA-C			Pathogenic (Aug 04, 2023)
X-22168383-C-CA		Familial X-linked hypophosphatemic vitamin D refractory rickets	Likely pathogenic (May 22, 2022)
X-22168388-C-G		not specified	Uncertain significance (Feb 27, 2024)
X-22168388-C-CT		Familial X-linked hypophosphatemic vitamin D refractory rickets	Pathogenic (May 04, 2022)
X-22168389-TG-T		Familial X-linked hypophosphatemic vitamin D refractory rickets	Likely pathogenic (-)

GnomAD

Source: gnomAD

dbNSFP

Source: dbNSFP