HNRNPLL

protein-coding

heterogeneous nuclear ribonucleoprotein L like, the group of RNA binding motif containing|Heterogeneous nuclear ribonucleoproteins

Gene summary

HNRNPLL is a master regulator of activation-induced alternative splicing in T cells. In particular, it alters splicing of CD45 (PTPRC; MIM 151460), a tyrosine phosphatase essential for T-cell development and activation (Oberdoerffer et al., 2008 [PubMed 18669861]).[supplied by OMIM, Aug 2008]

Previous symbols:

HNRPLL

MANE transcript

NM_138394.4

Inheritance

—

ClinVar variants

U:51

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.17

Max pathogenic AF

—

Genomic locus

chr2:38,561,969-38,603,586

External References & Databases

Ensembl (ENSG00000143889)

Transcript & Mutation Effects

hg38 • Region Span ~41.6 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 HNRNPLL variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 42

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_138394.4. 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			1 clinvar			1
missense			45 clinvar			45
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	51	0	0	51

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 26 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_138394.4	RefSeq	NP_612403.2	13	MANE Select
ENST00000449105.8	Ensembl	ENSP00000390625.3	13	MANE Select
NM_001142650.2	RefSeq	NP_001136122.1	14	Standard
ENST00000272249.7	Ensembl	ENSP00000272249.3	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

mRNA processing
positive regulation of RNA splicing

Molecular Function

RNA binding
mRNA binding
protein binding

Cellular Component

nucleus
membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000409636
Coding exons: 14
Length: 41609
Individuals with no LoFs: 125720
Homozygous LoFs: 0
Heterozygous LoFs: 23
Defined: 125743
p: 0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.36	177	290	0.610	0.0000149	3477
Missense (PolyPhen)		57	128.97	0.44197		1543
Synonymous	-1.36	122	104	1.17	0.00000525	1029
Loss of Function	4.24	5	30.1	0.166	0.00000169	368

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00019	0.00018	rare
Latino/Admixed American	0.00041	0.00040	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000053	0.000053	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: RNA-binding protein that functions as regulator of alternative splicing for multiple target mRNAs, including PTPRC/CD45 and STAT5A. Required for alternative splicing of PTPRC. {ECO:0000269|PubMed:18669861}.;

Recessive Scores

pRec: 0.109

Intolerance Scores

RVIS EVS: -0.34
RVIS percentile EVS: 30.37

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