PTCHD3 patched domain containing 3 (gene/pseudogene) [Homo sapiens (human)] - Gene

Summary

Official Symbol: PTCHD3provided by HGNC
Official Full Name: patched domain containing 3 (gene/pseudogene)provided by HGNC
Primary source: HGNC:HGNC:24776
See related: Ensembl:ENSG00000182077 MIM:611791; AllianceGenome:HGNC:24776
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: PTR
Summary: Located in endoplasmic reticulum and sperm midpiece. [provided by Alliance of Genome Resources, Dec 2024]
Annotation information: Annotation category: suggests misassembly
Expression: Restricted expression toward testis (RPKM 3.3) See more
Orthologs: mouse all
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Genomic context

Location:: 10p12.1

Exon count:: 4

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	10	NC_000010.11 (27397121..27414347, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	10	NC_060934.1 (27427292..27444622, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	10	NC_000010.10 (27686050..27703276, complement)

Chromosome 10 - NC_000010.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

PTCHD3 nulls: rare copy number and sequence variants suggest a non-essential gene.
Title: Human PTCHD3 nulls: rare copy number and sequence variants suggest a non-essential gene.
Results indicate that Ptchd3 is a novel male germ cell-specific gene and may be involved in the Hh signaling to regulate sperm development and/or sperm function.
Title: Male germ cell-specific expression of a novel Patched-domain containing gene Ptchd3.

Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
A genome-wide approach accounting for body mass index identifies genetic variants influencing fasting glycemic traits and insulin resistance. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Component	Evidence Code	Pubs
located_in endoplasmic reticulum	IDA Inferred from Direct Assay more info	PubMed
located_in endoplasmic reticulum membrane	IEA Inferred from Electronic Annotation more info
is_active_in membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	IEA Inferred from Electronic Annotation more info
located_in sperm midpiece	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: patched domain-containing protein 3

Names: patched-related protein

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_001034842.5 → NP_001030014.2 patched domain-containing protein 3 isoform 1

See identical proteins and their annotated locations for NP_001030014.2

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the allele encoded by the reference genome (GRCh38) and encodes isoform 1.

Source sequence(s)

AL355493

UniProtKB/TrEMBL

A0A8Q3VUI5

Related

ENSP00000495205.1, ENST00000642324.1

Conserved Domains (3) summary

pfam02460
Location:171 → 734

Patched; Patched family

pfam15240
Location:6 → 88

Pro-rich; Proline-rich

cl21543
Location:407 → 553

MMPL; MMPL family
NM_001395743.1 → NP_001382672.1 patched domain-containing protein 3 isoform 2

Status: VALIDATED

Description

Transcript Variant: This variant (2) retains a mismatch (C vs. T), at 27,398,296 compared to the reference genome sequence which results in the loss of a stop codon, compared to variant 1. The resulting isoform (2) has a longer C-terminus, compared to isoform 1.

Source sequence(s)

AK126025, AL355493

UniProtKB/Swiss-Prot

F6LPT1, I3L499, Q3KNS1, Q6ZU28

Conserved Domains (1) summary

cl25655
Location:171 → 952

Patched; Patched family