PID1

phosphotyrosine interaction domain containing 1

Basic information

Region (hg38): 2:228850526-229271287

Links

ENSG00000153823 ∙ NCBI:55022 ∙ OMIM:612930 ∙ HGNC:26084 ∙ Uniprot:Q7Z2X4 ∙ 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 PID1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PID1 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			11	2		13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	2	0

Variants in PID1

This is a list of pathogenic ClinVar variants found in the PID1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-229025670-C-T		not specified	Uncertain significance (Jul 19, 2023)
2-229025694-G-A		not specified	Uncertain significance (Feb 10, 2022)
2-229025700-C-T		Moyamoya angiopathy	Likely pathogenic (-)
2-229025712-T-C		not specified	Uncertain significance (Dec 07, 2021)
2-229025741-A-G		not specified	Uncertain significance (Dec 16, 2023)
2-229025798-T-A		not specified	Uncertain significance (Sep 20, 2023)
2-229025804-T-C		not specified	Uncertain significance (Aug 02, 2022)
2-229025910-C-G		not specified	Uncertain significance (Apr 07, 2022)
2-229025921-G-A		not specified	Uncertain significance (Mar 26, 2024)
2-229026017-G-A		PID1-related disorder	Likely benign (Mar 20, 2023)
2-229026025-C-A		not specified	Uncertain significance (Jul 12, 2023)
2-229026108-C-T		not specified	Uncertain significance (Nov 22, 2023)
2-229155889-G-A		not specified	Uncertain significance (Mar 12, 2024)
2-229155950-C-T		not specified	Uncertain significance (Mar 07, 2024)
2-229271028-T-C		PID1-related disorder	Likely benign (Nov 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PID1	protein_coding	protein_coding	ENST00000392054	3	420760

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00315	0.834	125686	0	3	125689	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.269	138	147	0.938	0.00000871	1658
Missense in Polyphen		48	61.232	0.7839		642
Synonymous	-0.0667	66	65.3	1.01	0.00000469	469
Loss of Function	1.16	5	8.68	0.576	4.55e-7	99

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.000101	0.0000993
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Increases proliferation of preadipocytes without affecting adipocytic differentiation. {ECO:0000269|PubMed:16815647}.

Recessive Scores

• pRec: 0.109

Intolerance Scores

• loftool: 0.0462
• rvis_EVS: -0.34
• rvis_percentile_EVS: 30.37

Haploinsufficiency Scores

• pHI: 0.213
• hipred: N
• hipred_score: 0.332
• ghis: 0.597

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0883

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pid1

Gene ontology

• Biological process: negative regulation of protein phosphorylation;energy reserve metabolic process;positive regulation of gene expression;regulation of mitochondrial fusion;cellular response to leptin stimulus;fat cell differentiation;positive regulation of transcription by RNA polymerase II;negative regulation of glucose import;negative regulation of insulin receptor signaling pathway;regulation of mitochondrial membrane potential;positive regulation of fat cell proliferation;mitochondrion morphogenesis;cellular response to cytokine stimulus;cellular response to interleukin-6;cellular response to tumor necrosis factor;cellular response to fatty acid;negative regulation of protein localization to plasma membrane;regulation of reactive oxygen species metabolic process;positive regulation of reactive oxygen species metabolic process;negative regulation of ATP biosynthetic process;positive regulation of ATP biosynthetic process
• Cellular component: cytoplasm
• Molecular function: protein binding