HNRNPA3

Chr 2

heterogeneous nuclear ribonucleoprotein A3

Also known as: 2610510D13Rik, D10S102, FBRNP, HNRPA3

NCBI Gene: 220988 ENSG00000170144 UniProt: P51991 OMIM: 605372

Enables RNA binding activity. Predicted to be involved in mRNA splicing, via spliceosome. Located in nucleus. Part of catalytic step 2 spliceosome. [provided by Alliance of Genome Resources, Jul 2025]

OMIM Research

OMIM ResearchGenerating clinical summary…

LOFmechanismLOEUF 0.23

Clinical Summary— HNRNPA3

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Population Constraint (gnomAD)

Highly constrained gene — heterozygous loss-of-function variants are very rare in the population (pLI 1.00). One damaged copy is likely sufficient to cause disease.

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ClinVar Variants

16 VUS of 35 total submissions

Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Dual constrained — LoF & missense intolerant

LoF Constraint?

0.23LOEUF

pLI 0.995

Z-score 3.98

OE 0.05 (0.02–0.23)

Highly constrained

Highly LoF-intolerant (top ~10% of genes)

Missense Constraint?

3.64Z-score

OE missense 0.30 (0.24–0.37)

63 obs / 212.0 exp

Constrained

Highly missense-constrained (top ~0.1%)

Observed / Expected Ratios?

LoF OE?0.05 (0.02–0.23)

0≤0.351.4

Missense OE?0.30 (0.24–0.37)

0≤0.61.4

Synonymous OE?1.21

0≤1.21.6

LoF obs/exp: 1 / 20.4Missense obs/exp: 63 / 212.0Syn Z: -1.37

This gene — mechanism propensity

0.4389th %ile

GOF

0.3689th %ile

LOF

0.79top 5%

The highest-scoring mechanism for this gene is loss-of-function (haploinsufficiency).

LOFprediction above median · LOEUF 0.23

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312. Mechanism ranking also informed by gnomAD constraint, ClinVar, and ClinGen data.

ClinVar Variant Classifications

35 submitted variants in ClinVar

ClinVar

Classification Summary

VUS16

VUS

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	LoF	Missense + Inframe	Total
Pathogenic	0	0	0
Likely Pathogenic	0	0	0
VUS	1	15	16
Likely Benign	0	0	0
Benign	0	0	0
Total	1	15	16

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

View in ClinVar →

30 pathogenic / likely-pathogenic (of 32) ClinVar copy-number / structural variants overlap HNRNPA3 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →