PITHD1

PITH domain containing 1

Basic information

Region (hg38): 1:23778417-23788232

Previous symbols: [ "C1orf128" ]

Links

ENSG00000057757 ∙ NCBI:57095 ∙ OMIM:618784 ∙ HGNC:25022 ∙ Uniprot:Q9GZP4 ∙ 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 PITHD1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PITHD1 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			9			9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	0	0

Variants in PITHD1

This is a list of pathogenic ClinVar variants found in the PITHD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-23778552-C-T		not specified	Uncertain significance (Feb 15, 2023)
1-23778655-G-T		not specified	Uncertain significance (Dec 05, 2022)
1-23778670-G-T		not specified	Uncertain significance (Sep 06, 2022)
1-23778672-G-A		not specified	Uncertain significance (Aug 17, 2021)
1-23779869-C-A		not specified	Uncertain significance (Oct 26, 2022)
1-23786370-G-A		not specified	Uncertain significance (Dec 14, 2023)
1-23787303-A-G		not specified	Uncertain significance (Oct 26, 2022)
1-23787342-A-G		not specified	Uncertain significance (Oct 06, 2021)
1-23787363-A-G		not specified	Uncertain significance (May 13, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PITHD1	protein_coding	protein_coding	ENST00000246151	6	9828

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00809	0.936	125737	0	11	125748	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.23	66	101	0.656	0.00000540	1379
Missense in Polyphen		23	38.021	0.60492		522
Synonymous	0.0282	36	36.2	0.994	0.00000202	391
Loss of Function	1.65	5	10.9	0.459	6.45e-7	134

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000153	0.000152
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000531	0.0000527
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.118

Haploinsufficiency Scores

• pHI: 0.241
• hipred: Y
• hipred_score: 0.607
• ghis: 0.673

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pithd1

Gene ontology

• Cellular component: nucleus