PIH1D1

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

Basic information

Region (hg38): 19:49446297-49453497

Previous symbols: [ "NOP17" ]

Links

ENSG00000104872 ∙ NCBI:55011 ∙ OMIM:611480 ∙ HGNC:26075 ∙ Uniprot:Q9NWS0 ∙ 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 PIH1D1 gene.

• Inborn genetic diseases (13 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PIH1D1 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			13			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	13	0	0

Variants in PIH1D1

This is a list of pathogenic ClinVar variants found in the PIH1D1 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-49446420-A-C		not specified	Uncertain significance (Feb 12, 2024)
19-49446591-T-G		not specified	Uncertain significance (Feb 28, 2023)
19-49446596-C-A		not specified	Uncertain significance (Jul 15, 2021)
19-49446598-G-T		not specified	Uncertain significance (Feb 05, 2024)
19-49446654-C-T		not specified	Uncertain significance (May 05, 2023)
19-49447365-G-A		not specified	Uncertain significance (Jul 08, 2022)
19-49447396-G-A		not specified	Uncertain significance (Oct 02, 2023)
19-49447419-T-C		not specified	Uncertain significance (Dec 13, 2021)
19-49447446-C-T		not specified	Uncertain significance (May 09, 2023)
19-49447461-C-T		not specified	Uncertain significance (Dec 07, 2021)
19-49447865-T-A		not specified	Uncertain significance (May 05, 2023)
19-49447875-T-A		not specified	Uncertain significance (Apr 07, 2023)
19-49448038-T-G		not specified	Uncertain significance (Aug 02, 2023)
19-49449489-G-T		not specified	Uncertain significance (Apr 11, 2023)
19-49449516-A-G		not specified	Uncertain significance (Dec 15, 2023)
19-49449562-C-T		not specified	Uncertain significance (Oct 26, 2022)
19-49449600-T-C		not specified	Uncertain significance (Aug 14, 2023)
19-49450806-A-T		not specified	Uncertain significance (Jan 30, 2024)
19-49453356-C-A		not specified	Likely benign (Jul 05, 2023)
19-49453359-G-C		not specified	Uncertain significance (Mar 01, 2024)
19-49453398-C-T		not specified	Uncertain significance (Jan 13, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PIH1D1	protein_coding	protein_coding	ENST00000262265	9	7200

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000107	0.952	125729	0	17	125746	0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.643	162	187	0.868	0.0000117	1874
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000123	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000552	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000107	0.000105
Middle Eastern	0.0000552	0.0000544
South Asian	0.0000327	0.0000327
Other	0.000163	0.000163

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.134
• hipred: Y
• hipred_score: 0.731
• ghis: 0.408

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.974

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pih1d1

Gene ontology

• Biological process: box C/D snoRNP assembly;RNA polymerase I preinitiation complex assembly;chromatin remodeling;rRNA processing;epithelial cell differentiation;positive regulation of protein complex assembly;snoRNA localization;regulation of histone H3-K4 methylation;establishment of protein localization to chromatin;positive regulation of protein serine/threonine kinase activity;positive regulation of histone H4 acetylation;negative regulation of histone H3-K9 dimethylation;negative regulation of histone H3-K9 trimethylation;positive regulation of transcription of nucleolar large rRNA by RNA polymerase I;positive regulation of glucose mediated signaling pathway;regulation of TORC2 signaling;positive regulation of TORC1 signaling;positive regulation of histone H3-K9 acetylation;negative regulation of histone H4-K16 acetylation;negative regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway
• Cellular component: nucleus;nucleolus;cytoplasm;pre-snoRNP complex;R2TP complex
• 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;ATPase binding;phosphoprotein binding