PRAC1

protein-coding

PRAC1 small nuclear protein

Gene summary

This gene is reported to be specifically expressed in prostate, rectum and distal colon. Sequence analysis suggests that it may play a regulatory role in the nucleus. [provided by RefSeq, Jul 2008]

Previous symbols:

C17orf92
PRAC

MANE transcript

NM_032391.3

Inheritance

—

ClinVar variants

U:8B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.59

Max pathogenic AF

—

Genomic locus

chr17:48,721,719-48,722,518

External References & Databases

Ensembl (ENSG00000159182)

Transcript & Mutation Effects

hg38 • Region Span ~0.8 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 PRAC1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 8

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_032391.3. 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						0
missense			8 clinvar		1 clinvar	9
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	8	0	1	9

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 11 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_032391.3	RefSeq	NP_115767.1	2	MANE Select
ENST00000290294.5	Ensembl	ENSP00000290294.3	2	MANE Select
ENST00000936891.1	Ensembl	ENSP00000606950.1	2	Standard
ENST00000936891.2	Ensembl	ENSP00000606950.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000290294
Coding exons: 2
Length: 801
Individuals with no LoFs: 125717
Homozygous LoFs: 0
Heterozygous LoFs: 7
Defined: 125724
p: 0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.326	31	26.3	1.18	0.00000126	356
Missense (PolyPhen)		7	3.6988	1.8925		42
Synonymous	0.151	10	10.6	0.941	5.34e-7	120
Loss of Function	-0.616	2	1.26	1.59	5.33e-8	16

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000018	0.000018	rare
South Asian	0.000098	0.000098	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

RVIS EVS: 0.46
RVIS percentile EVS: 78.16

Essentials

Essential (CRISPR): N
Essential (gene trap): N

Gene Damage Prediction

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