HNRNPCL1

protein-coding

heterogeneous nuclear ribonucleoprotein C like 1, the group of RNA binding motif containing

Gene summary

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]

Previous symbols:

HNRPCL1

MANE transcript

NM_001013631.3

Inheritance

—

ClinVar variants

U:45B:7

Top phenotype

Mayer-Rokitansky-Kuster-Hauser syndrome

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chr1:12,847,377-12,848,720

External References & Databases

Ensembl (ENSG00000179172)

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 HNRNPCL1 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 45

not providedTotal: 6

Mayer-Rokitansky-Kuster-Hauser syndromeTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001013631.3. 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				5 clinvar		5
missense			44 clinvar	2 clinvar		46
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)						0
Total	0	0	45	7	0	52

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 2 of 2 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001013631.3	RefSeq	NP_001013653.1	1	MANE Select
ENST00000317869.7	Ensembl	ENSP00000365370.4	1	MANE Select

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

RNA binding

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000317869
Coding exons: 1
Length: 1318
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-1.38	183	138	1.33	0.00000814	1802
Missense (PolyPhen)		15	15.023	0.99848		255
Synonymous	0.324	46	48.9	0.941	0.00000265	492
Loss of Function	0.841	0	0.824	0.00	3.44e-8	18

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May play a role in nucleosome assembly by neutralizing basic proteins such as A and B core hnRNPs. {ECO:0000250}.;

Intolerance Scores

LoFtool: 0.881
RVIS EVS: 1.19
RVIS percentile EVS: 92.89

Essentials

Essential (CRISPR): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0778

Gene Damage Prediction

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