HNRNPA1L2

Chr 13

heterogeneous nuclear ribonucleoprotein A1 like 2

NCBI Gene: 144983 ENSG00000139675 UniProt: Q32P51

HNRNPA1L2 encodes a heterogeneous nuclear ribonucleoprotein that binds RNA and is involved in pre-mRNA packaging, mRNA splicing regulation, and transport of polyadenylated mRNA from nucleus to cytoplasm. The gene shows low constraint against loss-of-function variants (pLI 0.02, LOEUF 1.91), and no established disease associations have been reported to date. This gene remains under investigation for potential clinical significance in neurogenetic disorders.

ResearchSummary from RefSeq, UniProt

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]

ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.91

LOEUF

Mechanism· predicted

Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.91LOEUF

pLI 0.019

Z-score -0.36

OE 1.32 (0.43–1.91)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

-0.07Z-score

OE missense 1.01 (0.90–1.15)

178 obs / 175.5 exp

Tolerant

Tolerant to missense variation

Observed / Expected Ratios?

LoF OE?1.32 (0.43–1.91)

0≤0.351.4

Missense OE?1.01 (0.90–1.15)

0≤0.61.4

Synonymous OE?1.07

0≤1.21.6

LoF obs/exp: 2 / 1.5Missense obs/exp: 178 / 175.5Syn Z: -0.46

Background carrier burden — how many people carry a rare variant somewhere in HNRNPA1L2?

gnomAD v4 · ~730k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 94

335 rare PASS variants

Rare truncating (LoF)

1 in 2,600

28 rare PASS variants

Rare synonymous (reference)

1 in 380

140 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for HNRNPA1L2. A background rate for each class, not the frequency of any particular variant; thin-coverage exons undercount.

By genetic ancestry · 9 gnomAD groups · rare = under 0.1% in that group

Group	People	Missense	Truncating
European (non-Finnish)	~556k	1 in 150	1 in 5,000
South Asian	~43k	1 in 88	1 in 1,500
Remaining (unassigned)	~30k	1 in 81	1 in 1,500
European (Finnish)	~27k	1 in 560	none seen
Admixed American	~22k	1 in 74	1 in 2,000
African / African American	~21k	1 in 120	1 in 1,600
East Asian	~20k	1 in 110	1 in 600
Ashkenazi Jewish	~13k	1 in 590	≈ 1 in 6,500
Middle Eastern	~2,650	1 in 150	≈ 1 in 1,100

Each group is summed over the variants that are rare in that group. Grey ≈ figures rest on fewer than five expected carriers — too few to distinguish groups. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.

Exome coverage (gnomAD): All 1 coding exons well covered in gnomAD exomes and genomes.? see exons ↓