PASD1

PAS domain containing repressor 1, the group of PAS domain containing

Basic information

Region (hg38): X:151563674-151676739

Links

ENSG00000166049 ∙ NCBI:139135 ∙ OMIM:300993 ∙ HGNC:20686 ∙ Uniprot:Q8IV76 ∙ 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 PASD1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PASD1 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				2		2
missense			34	10	1	45
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	34	12	1

Variants in PASD1

This is a list of pathogenic ClinVar variants found in the PASD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-151601567-G-A		not specified	Likely benign (Mar 07, 2023)
X-151601572-A-G		not specified	Uncertain significance (Feb 15, 2023)
X-151620960-C-T		not specified	Likely benign (Jul 12, 2022)
X-151620994-A-G		not specified	Uncertain significance (Jun 16, 2024)
X-151621001-T-G		not specified	Uncertain significance (Aug 30, 2021)
X-151621026-T-G		not specified	Uncertain significance (Apr 05, 2023)
X-151621523-G-A		not specified	Uncertain significance (May 31, 2023)
X-151622942-C-T		not specified	Uncertain significance (Oct 17, 2023)
X-151622998-T-G		not specified	Uncertain significance (Dec 11, 2023)
X-151623003-C-G		not specified	Uncertain significance (Oct 25, 2023)
X-151623020-T-C		not specified	Uncertain significance (Mar 30, 2024)
X-151623044-C-T		not specified	Uncertain significance (Apr 21, 2022)
X-151623054-A-G		not specified	Uncertain significance (Oct 02, 2023)
X-151625461-C-T		not specified	Uncertain significance (May 20, 2024)
X-151648698-C-T		not specified	Likely benign (Dec 20, 2022)
X-151659735-T-C		not specified	Uncertain significance (May 27, 2022)
X-151664177-C-A		not specified	Likely benign (Jun 24, 2022)
X-151664203-A-G		not specified	Uncertain significance (Nov 09, 2023)
X-151664235-A-G			Benign (May 01, 2022)
X-151664236-T-G		not specified	Uncertain significance (Feb 23, 2023)
X-151664311-A-G		not specified	Uncertain significance (Dec 15, 2022)
X-151664337-G-T		not specified	Uncertain significance (Oct 12, 2021)
X-151671122-G-A		not specified	Likely benign (Feb 06, 2024)
X-151671129-C-T		not specified	Uncertain significance (Oct 27, 2023)
X-151671153-A-C		not specified	Uncertain significance (Dec 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PASD1	protein_coding	protein_coding	ENST00000370357	15	113118

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.823	0.177	125098	0	3	125101	0.0000120

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.812	319	281	1.14	0.0000210	5084
Missense in Polyphen		24	30.475	0.78753		619
Synonymous	-1.05	125	111	1.13	0.00000885	1422
Loss of Function	4.00	5	27.7	0.180	0.00000190	485

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000783	0.0000616
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000727	0.0000545
Finnish	0.00	0.00
European (Non-Finnish)	0.0000126	0.00000882
Middle Eastern	0.0000727	0.0000545
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Functions as a suppressor of the biological clock that drives the daily circadian rhythms of cells throughout the body (PubMed:25936801). Acts as a nuclear repressor of the CLOCK- ARNTL/BMAL1 heterodimer-mediated transcriptional activation of the core clock components (PubMed:25936801). Inhibits circadian clock function in cancer cells, when overexpressed (PubMed:25936801). {ECO:0000269|PubMed:25936801}.

Recessive Scores

• pRec: 0.0654

Intolerance Scores

• loftool: 0.385
• rvis_EVS: 0.38
• rvis_percentile_EVS: 75.63

Haploinsufficiency Scores

• pHI: 0.0554
• hipred: N
• hipred_score: 0.316

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0346

Gene Damage Prediction

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

Gene ontology

• Biological process: negative regulation of circadian rhythm;negative regulation of transcription, DNA-templated;rhythmic process
• Cellular component: nucleus;nuclear speck;Cry-Per complex
• Molecular function: transcription coactivator binding