PDILT

protein disulfide isomerase like, testis expressed, the group of Protein disulfide isomerases

Basic information

Region (hg38): 16:20359175-20404737

Links

ENSG00000169340 ∙ NCBI:204474 ∙ OMIM:618588 ∙ HGNC:27338 ∙ Uniprot:Q8N807 ∙ 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 PDILT gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PDILT 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			63	6		69
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	63	7	0

Variants in PDILT

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

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

Position	Type	Phenotype	Significance	ClinVar
16-20359356-A-C		not specified	Uncertain significance (Dec 20, 2023)
16-20359360-G-A		not specified	Uncertain significance (Jan 04, 2024)
16-20359363-G-A		not specified	Uncertain significance (Mar 28, 2023)
16-20359374-T-A		not specified	Uncertain significance (Jul 14, 2021)
16-20359404-G-A		not specified	Uncertain significance (Aug 21, 2024)
16-20359413-T-C		not specified	Uncertain significance (Jan 25, 2023)
16-20359422-G-A		not specified	Uncertain significance (Jan 23, 2024)
16-20359446-T-C		not specified	Uncertain significance (Jul 25, 2024)
16-20359451-C-A		not specified	Uncertain significance (Feb 23, 2023)
16-20359470-G-A		not specified	Likely benign (Oct 26, 2021)
16-20359477-G-C		not specified	Uncertain significance (Jan 05, 2022)
16-20359558-C-A		not specified	Uncertain significance (Jul 14, 2024)
16-20360584-A-G		not specified	Uncertain significance (May 31, 2023)
16-20360597-T-C		not specified	Likely benign (Aug 21, 2024)
16-20362415-C-T		not specified	Uncertain significance (Dec 08, 2021)
16-20362428-C-G		not specified	Uncertain significance (Aug 01, 2022)
16-20362466-T-G		not specified	Uncertain significance (Oct 07, 2024)
16-20362485-G-A		not specified	Likely benign (Nov 25, 2024)
16-20362504-G-A		not specified	Uncertain significance (May 01, 2022)
16-20362512-G-T		not specified	Uncertain significance (Sep 08, 2024)
16-20362541-A-T		not specified	Uncertain significance (Mar 20, 2023)
16-20362555-A-T		not specified	Uncertain significance (Dec 03, 2021)
16-20365438-C-T		not specified	Uncertain significance (Jun 24, 2022)
16-20365462-C-T		not specified	Likely benign (Jan 24, 2023)
16-20365470-T-A		not specified	Uncertain significance (Jul 15, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PDILT	protein_coding	protein_coding	ENST00000302451	11	45568

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000122	0.990	125710	0	38	125748	0.000151

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.396	342	322	1.06	0.0000184	3881
Missense in Polyphen		99	105.67	0.93688		1388
Synonymous	-1.21	149	131	1.13	0.00000838	1093
Loss of Function	2.30	12	24.2	0.495	0.00000123	291

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000667	0.000667
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000114	0.000114
Middle Eastern	0.0000544	0.0000544
South Asian	0.000431	0.000294
Other	0.000329	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable redox-inactive chaperone involved in spermatogenesis. {ECO:0000269|PubMed:17507649}.

Intolerance Scores

• loftool: 0.767
• rvis_EVS: 0.79
• rvis_percentile_EVS: 87.29

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.173

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0410

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pdilt
• Phenotype: reproductive system phenotype

Gene ontology

• Biological process: protein folding;multicellular organism development;spermatid development;cell migration;peptidyl-proline hydroxylation;cell redox homeostasis
• Cellular component: endoplasmic reticulum