PIH1D1

protein-coding

PIH1 domain containing 1, the group of Axonemal dynein assembly factors|R2TP complex

Gene summary

Enables several functions, including enzyme binding activity; histone binding activity; and phosphoprotein binding activity. Involved in several processes, including positive regulation of signal transduction; positive regulation of transcription of nucleolar large rRNA by RNA polymerase I; and protein-containing complex assembly. Located in cytoplasm and nucleolus. Part of R2TP complex and pre-snoRNP complex. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

NOP17

MANE transcript

NM_017916.3

Inheritance

—

ClinVar variants

U:48

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.53

Max pathogenic AF

—

Genomic locus

chr19:49,446,298-49,453,497

External References & Databases

Ensembl (ENSG00000104872)

Transcript & Mutation Effects

hg38 • Region Span ~7.2 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 PIH1D1 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 41

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_017916.3. 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			2 clinvar			2
missense			42 clinvar			42
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	48	0	0	48

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 47 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_017916.3	RefSeq	NP_060386.1	9	MANE Select
ENST00000262265.10	Ensembl	ENSP00000262265.4	9	MANE Select
ENST00000594845.5	Ensembl	ENSP00000470322.1	3	Standard
ENST00000595550.1	Ensembl	ENSP00000472571.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

box C/D snoRNP assembly
RNA polymerase I preinitiation complex assembly
chromatin remodeling
rRNA processing
epithelial cell differentiation

Molecular Function

RNA polymerase I CORE element sequence-specific DNA binding
RNA polymerase I upstream control element sequence-specific DNA binding
protein binding
protein kinase binding
histone binding

Cellular Component

nucleus
nucleolus
cytoplasm
pre-snoRNP complex
R2TP complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000262265
Coding exons: 9
Length: 7200
Individuals with no LoFs: 125729
Homozygous LoFs: 0
Heterozygous LoFs: 17
Defined: 125746
p: 0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.643	162	187	0.868	0.0000117	1874
Missense (PolyPhen)		34	55.264	0.61523		591
Synonymous	0.199	81	83.3	0.972	0.00000584	575
Loss of Function	1.78	9	16.9	0.532	7.21e-7	187

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000055	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00011	0.00011	rare
South Asian	0.000033	0.000033	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Involved in the assembly of C/D box small nucleolar ribonucleoprotein (snoRNP) particles (PubMed:17636026). Recruits the SWI/SNF complex to the core promoter of rRNA genes and enhances pre-rRNA transcription (PubMed:22368283, PubMed:24036451). Mediates interaction of TELO2 with the R2TP complex which is necessary for the stability of MTOR and SMG1 (PubMed:20864032). Positively regulates the assembly and activity of the mTORC1 complex (PubMed:24036451). {ECO:0000269|PubMed:17636026, ECO:0000269|PubMed:20864032, ECO:0000269|PubMed:22368283, ECO:0000269|PubMed:24036451}.;

Recessive Scores

pRec: 0.104

Intolerance Scores

LoFtool: 0.582
RVIS EVS: 0.86
RVIS percentile EVS: 88.69

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.974

Gene Damage Prediction

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