PTBP3

protein-coding

polypyrimidine tract binding protein 3, the group of RNA binding motif containing

Gene summary

The protein encoded by this gene binds RNA and is a regulator of cell differentiation. The encoded protein preferentially binds to poly(G) and poly(U) sequences in vitro. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2011]

Previous symbols:

ROD1

MANE transcript

NM_001163788.4

Inheritance

—

ClinVar variants

U:59

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.18

Max pathogenic AF

—

Genomic locus

chr9:112,217,716-112,333,664

External References & Databases

Ensembl (ENSG00000119314)

Transcript & Mutation Effects

hg38 • Region Span ~115.9 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 PTBP3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 60

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001163788.4. 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			59 clinvar			59
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	59	0	0	59

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 54 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001163788.4	RefSeq	NP_001157260.1	13	MANE Select
ENST00000374257.6	Ensembl	ENSP00000363375.1	13	MANE Select
NM_001163790.2	RefSeq	NP_001157262.1	15	Standard
NM_001244896.2	RefSeq	NP_001231825.1	12	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

mRNA processing
RNA splicing
anatomical structure morphogenesis
negative regulation of RNA splicing
erythrocyte maturation

Molecular Function

RNA binding

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000458258
Coding exons: 14
Length: 115233
Individuals with no LoFs: 125723
Homozygous LoFs: 0
Heterozygous LoFs: 23
Defined: 125746
p: 0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.20	242	301	0.805	0.0000153	3621
Missense (PolyPhen)		30	52.675	0.56953		723
Synonymous	0.184	103	105	0.977	0.00000539	1130
Loss of Function	4.08	5	28.5	0.175	0.00000181	311

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00037	0.00037	rare
Latino/Admixed American	0.000093	0.000087	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0.00014	0.00014	rare
European (Non-Finnish)	0.000071	0.000070	rare
South Asian	0	0.0	absent
Other	0.00049	0.00049	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: RNA-binding protein that mediates pre-mRNA alternative splicing regulation. Plays a role in the regulation of cell proliferation, differentiation and migration. Positive regulator of EPO-dependent erythropoiesis. Participates in cell differentiation regulation by repressing tissue-specific exons. Promotes FAS exon 6 skipping. Binds RNA, preferentially to both poly(G) and poly(U). {ECO:0000269|PubMed:10207106, ECO:0000269|PubMed:18335065, ECO:0000269|PubMed:19441079, ECO:0000269|PubMed:20937273}.;

Recessive Scores

pRec: 0.0949

Intolerance Scores

RVIS EVS: -0.62
RVIS percentile EVS: 17.16

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

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