HNRNPA1L2

Chr 13

heterogeneous nuclear ribonucleoprotein A1 like 2

NCBI Gene: 144983ENSG00000139675UniProt: 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
DNmechanismLOEUF 1.91
Clinical Summary— HNRNPA1L2
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.02) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
58 unique Pathogenic / Likely Pathogenic· 60 VUS of 132 total submissions
Explore recent and relevant literature in Research Assistant →

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 OE1.32 (0.43–1.91)
0≤0.351.4
Missense OE1.01 (0.90–1.15)
0≤0.61.4
Synonymous OE1.07
0≤1.21.6
LoF obs/exp: 2 / 1.5Missense obs/exp: 178 / 175.5Syn Z: -0.46
DN
0.82top 10%
GOF
0.5857th %ile
LOF
0.3647th %ile

The highest-scoring mechanism for this gene is dominant-negative.

DNprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

132 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic56
Likely Pathogenic2
VUS60
56
Pathogenic
2
Likely Pathogenic
60
VUS

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
56
0
56
Likely Pathogenic
0
0
2
0
2
VUS
0
49
11
0
60
Likely Benign
0
0
0
0
0
Benign
0
0
0
0
0
Total049690118

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

HNRNPA1L2 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

3D Protein StructureAlphaFold

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →
Clinical Literature
Open Research Assistant →
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 5 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Top 2 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC

No open access results found

Top 5 resultsSearch Europe PMC ↗

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients