PIH1D2

PIH1 domain containing 2, the group of R2SP complex|Axonemal dynein assembly factors

Basic information

Region (hg38): 11:112063218-112074274

Links

ENSG00000150773 ∙ NCBI:120379 ∙ ∙ HGNC:25210 ∙ Uniprot:Q8WWB5 ∙ 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 PIH1D2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PIH1D2 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			10	2		12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	2	0

Variants in PIH1D2

This is a list of pathogenic ClinVar variants found in the PIH1D2 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-112064196-G-A		not specified	Uncertain significance (Sep 01, 2021)
11-112067978-T-G		not specified	Uncertain significance (Jun 17, 2024)
11-112067980-T-A		not specified	Uncertain significance (Feb 05, 2024)
11-112070537-T-G		not specified	Uncertain significance (Dec 13, 2021)
11-112070559-C-T		not specified	Likely benign (May 18, 2022)
11-112070608-G-A		not specified	Uncertain significance (Nov 08, 2022)
11-112070614-C-G		not specified	Uncertain significance (Jul 13, 2021)
11-112070638-A-G		not specified	Uncertain significance (Oct 04, 2022)
11-112070656-T-C		not specified	Uncertain significance (May 18, 2022)
11-112071112-C-G		not specified	Uncertain significance (Feb 06, 2023)
11-112071113-T-G		not specified	Uncertain significance (Oct 30, 2023)
11-112071158-T-A		not specified	Uncertain significance (Sep 26, 2023)
11-112071692-T-C		not specified	Likely benign (Feb 13, 2024)
11-112073102-T-G		not specified	Uncertain significance (Sep 16, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PIH1D2	protein_coding	protein_coding	ENST00000280350	5	10265

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.55e-9	0.152	125680	0	68	125748	0.000270

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.600	133	154	0.864	0.00000671	2075
Missense in Polyphen		28	34.642	0.80828		477
Synonymous	0.706	47	53.6	0.877	0.00000239	591
Loss of Function	0.225	13	13.9	0.935	6.87e-7	175

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000955	0.000955
Ashkenazi Jewish	0.000198	0.000198
East Asian	0.0000544	0.0000544
Finnish	0.0000925	0.0000924
European (Non-Finnish)	0.000247	0.000246
Middle Eastern	0.0000544	0.0000544
South Asian	0.000302	0.000294
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.916
• rvis_EVS: 0.64
• rvis_percentile_EVS: 83.78

Haploinsufficiency Scores

• pHI: 0.107
• hipred: N
• hipred_score: 0.123
• ghis: 0.454

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.158

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pih1d2

Gene ontology

• Biological process: box C/D snoRNP assembly;rRNA processing
• Cellular component: cytoplasm;R2TP complex
• Molecular function: protein binding;Ral GTPase binding