HNRNPA1L2

protein-coding

heterogeneous nuclear ribonucleoprotein A1 like 2, the group of Heterogeneous nuclear ribonucleoproteins|RNA binding motif containing

Gene summary

Predicted to enable mRNA 3'-UTR binding activity. Predicted to be involved in mRNA splicing, via spliceosome. Predicted to be located in cytoplasm and nucleus. Predicted to be part of catalytic step 2 spliceosome. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001389320.1

Inheritance

—

ClinVar variants

U:49

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.32

Max pathogenic AF

—

Genomic locus

chr13:52,642,431-52,643,773

External References & Databases

Ensembl (ENSG00000139675)

Transcript & Mutation Effects

hg38 • Region Span ~1.3 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 HNRNPA1L2 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 49

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001389320.1. 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			49 clinvar			49
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	49	0	0	49

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 4 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001389320.1	RefSeq	NP_001376249.1	1	MANE Select
ENST00000357495.5	Ensembl	ENSP00000350090.2	1	MANE Select
NM_001011724.3	RefSeq	NP_001011724.1	1	Standard
NM_001011725.3	RefSeq	NP_001011725.1	1	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Spliceosome - Homo sapiens (human)

Biological Process

mRNA processing
RNA splicing
mRNA transport

Molecular Function

RNA binding
mRNA binding

Cellular Component

nucleus
spliceosomal complex
cytoplasm
ribonucleoprotein complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000342657
Coding exons: 1
Length: 26315
Individuals with no LoFs: 124138
Homozygous LoFs: 8
Heterozygous LoFs: 1402
Defined: 125548
p: 0.00563

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.0677	178	175	1.01	0.00000914	2110
Missense (PolyPhen)		30	34.028	0.88163		465
Synonymous	-0.460	69	64.3	1.07	0.00000360	622
Loss of Function	-0.363	2	1.52	1.32	6.41e-8	20

Population LoF Frequency

Population	CAF	p-value	Status
African	0.018	0.017	notable
Latino/Admixed American	0.0034	0.0034	notable
Ashkenazi Jewish	0.0056	0.0056	notable
East Asian	0	0.0	absent
Finnish	0.0030	0.0031	notable
European (Non-Finnish)	0.0031	0.0031	notable
South Asian	0.017	0.017	notable
Other	0.0051	0.0051	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Involved in the packaging of pre-mRNA into hnRNP particles, transport of poly(A) mRNA from the nucleus to the cytoplasm and may modulate splice site selection. {ECO:0000250}.;

Recessive Scores

pRec: 0.0731

Intolerance Scores

LoFtool: 0.339
RVIS EVS: 1.31
RVIS percentile EVS: 94

Essentials

Essential (CRISPR): N
Indispensability pred.: N
Indispensability score: 0.231

Gene Damage Prediction

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