HNRNPCL1

Chr 1

heterogeneous nuclear ribonucleoprotein C like 1

Also known as: HNRPCL1

NCBI Gene: 343069 ENSG00000179172 UniProt: O60812

The protein enables identical protein binding activity and is predicted to function in ribonucleoprotein complexes within the nucleus, potentially involved in nucleosome assembly through neutralization of basic proteins. Currently, no established disease associations have been reported for mutations in this gene. The gene shows relatively low constraint to loss-of-function variation (pLI 0.37, LOEUF 1.77), suggesting tolerance to such variants in the general population.

ResearchSummary from RefSeq, UniProt

Enables identical protein binding activity. Predicted to be part of ribonucleoprotein complex. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Jul 2025]

ResearchGenerating clinical summary…

DNmechanismLOEUF 1.77

Clinical Summary— HNRNPCL1

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Population Constraint (gnomAD)

Constrained for loss-of-function variants (OE-LoF 0.00) despite low pLI — interpret in context.

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ClinVar Variants

44 VUS of 53 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?

1.77LOEUF

pLI 0.373

Z-score 0.84

OE 0.00 (0.00–1.77)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

-1.38Z-score

OE missense 1.33 (1.18–1.50)

183 obs / 137.6 exp

Tolerant

Tolerant to missense variation

Observed / Expected Ratios?

LoF OE?0.00 (0.00–1.77)

0≤0.351.4

Missense OE?1.33 (1.18–1.50)

0≤0.61.4

Synonymous OE?0.94

0≤1.21.6

LoF obs/exp: 0 / 0.8Missense obs/exp: 183 / 137.6Syn Z: 0.32

This gene — mechanism propensity

0.7131th %ile

GOF

0.4579th %ile

LOF

0.4726th %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

53 submitted variants in ClinVar

ClinVar

Classification Summary

VUS44

Likely Benign7

VUS

Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	LoF	Missense + Inframe	Synonymous	Total
Pathogenic	0	0	0	0
Likely Pathogenic	0	0	0	0
VUS	1	43	0	44
Likely Benign	0	2	5	7
Benign	0	0	0	0
Total	1	45	5	51

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

View in ClinVar →

31 pathogenic / likely-pathogenic (of 44) ClinVar copy-number / structural variants overlap HNRNPCL1 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →