PID1

protein-coding

phosphotyrosine interaction domain containing 1

Gene summary

Involved in several processes, including negative regulation of ATP biosynthetic process; negative regulation of D-glucose import across plasma membrane; and regulation of gene expression. Located in cytoplasm. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001100818.2

Inheritance

—

ClinVar variants

P:1U:34B:2

Top phenotype

PID1-related disorder

gnomAD constraint

pLI —, LoF o/e 0.58

Max pathogenic AF

—

Genomic locus

chr2:228,850,526-229,271,287

External References & Databases

Ensembl (ENSG00000153823)

Transcript & Mutation Effects

hg38 • Region Span ~420.8 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PID1 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 33

PID1-related disorderTotal: 2

Moyamoya angiopathyTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001100818.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar			1
missense		1 clinvar	33 clinvar	2 clinvar		36
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	1	34	2	0	37

Highest pathogenic variant AF is 0.000016108506

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 21 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001100818.2	RefSeq	NP_001094288.1	3	MANE Select
ENST00000392055.8	Ensembl	ENSP00000375908.3	3	MANE Select
NM_001330156.1	RefSeq	NP_001317085.1	3	Standard
NM_001330157.2	RefSeq	NP_001317086.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

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

Molecular Function

protein binding

Cellular Component

cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000392054
Coding exons: 3
Length: 420760
Individuals with no LoFs: 125686
Homozygous LoFs: 0
Heterozygous LoFs: 3
Defined: 125689
p: 0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.269	138	147	0.938	0.00000871	1658
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.000054	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0883

Gene Damage Prediction

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