PASD1

protein-coding

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

Gene summary

This gene encodes a protein that is thought to function as a transcription factor. The protein is a cancer-associated antigen that can stimulate autologous T-cell responses, and it is therefore considered to be a potential immunotherapeutic target for the treatment of various hematopoietic malignancies, including diffuse large B-cell lymphoma. [provided by RefSeq, May 2010]

MANE transcript

NM_173493.3

Inheritance

—

ClinVar variants

U:122B:22

Top phenotype

EBV-positive nodal T- and NK-cell lymphoma

gnomAD constraint

pLI —, LoF o/e 0.18

Max pathogenic AF

—

Genomic locus

chrX:151,563,675-151,676,739

External References & Databases

Ensembl (ENSG00000166049)

Transcript & Mutation Effects

hg38 • Region Span ~113.1 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 PASD1 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 122

not providedTotal: 3

EBV-positive nodal T- and NK-cell lymphomaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_173493.3. 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			115 clinvar	20 clinvar		135
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			6 clinvar			6
Total	0	0	122	22	0	144

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 3 of 3 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_173493.3	RefSeq	NP_775764.2	15	MANE Select
ENST00000370357.5	Ensembl	ENSP00000359382.4	15	MANE Select
XM_011531102.3	RefSeq	XP_011529404.1	15	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

negative regulation of circadian rhythm
negative regulation of transcription, DNA-templated
rhythmic process

Molecular Function

transcription coactivator binding

Cellular Component

nucleus
nuclear speck
Cry-Per complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000370357
Coding exons: 15
Length: 113118
Individuals with no LoFs: 125098
Homozygous LoFs: 0
Heterozygous LoFs: 3
Defined: 125101
p: 0.0000120

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.812	319	281	1.14	0.0000210	5084
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000078	0.000062	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000073	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000013	0.0000088	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0346

Gene Damage Prediction

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