HNRNPCL1

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

Basic information

Region (hg38): 1:12847377-12848720

Previous symbols: [ "HNRPCL1" ]

Links

ENSG00000179172 ∙ NCBI:343069 ∙ ∙ HGNC:29295 ∙ Uniprot:O60812 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the HNRNPCL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HNRNPCL1 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				3		3
missense			20	2		22
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	5	0

Variants in HNRNPCL1

This is a list of pathogenic ClinVar variants found in the HNRNPCL1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
1-12847461-C-T		not specified	Uncertain significance (Sep 10, 2024)
1-12847503-C-A		not specified	Uncertain significance (Feb 10, 2022)
1-12847512-C-T		not specified	Uncertain significance (Sep 02, 2024)
1-12847525-AT-A		Mayer-Rokitansky-Kuster-Hauser syndrome	Uncertain significance (Oct 12, 2016)
1-12847540-C-A		not specified	Uncertain significance (Jul 31, 2024)
1-12847543-C-G		not specified	Likely benign (May 26, 2024)
1-12847582-C-T			Likely benign (Jan 01, 2023)
1-12847690-G-C		not specified	Uncertain significance (Aug 02, 2023)
1-12847695-C-T		not specified	Uncertain significance (Jan 23, 2025)
1-12847700-A-G		not specified	Uncertain significance (Aug 11, 2022)
1-12847790-C-G		not specified	Uncertain significance (Dec 15, 2022)
1-12847790-C-T		not specified	Uncertain significance (Oct 01, 2024)
1-12847814-C-T		not specified	Uncertain significance (Apr 25, 2022)
1-12847848-G-T			Likely benign (Jan 01, 2024)
1-12847849-A-G			Likely benign (Jan 01, 2024)
1-12847855-A-G			Likely benign (Feb 01, 2024)
1-12847884-T-G		not specified	Uncertain significance (Dec 13, 2022)
1-12847899-G-A		not specified	Uncertain significance (Dec 23, 2024)
1-12847904-C-T		not specified	Uncertain significance (Dec 21, 2022)
1-12847922-A-G		not specified	Uncertain significance (Aug 19, 2024)
1-12847937-T-G		not specified	Uncertain significance (Jun 29, 2023)
1-12847949-C-A		not specified	Uncertain significance (Nov 14, 2024)
1-12847953-A-C		not specified	Uncertain significance (Jan 10, 2025)
1-12847957-C-A		not specified	Uncertain significance (Feb 23, 2023)
1-12848041-G-C		not specified	Uncertain significance (Dec 03, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HNRNPCL1	protein_coding	protein_coding	ENST00000317869	1	1318

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.373	0.489	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.38	183	138	1.33	0.00000814	1802
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.252
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0778

Gene Damage Prediction

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

Gene ontology

• Cellular component: nucleus
• Molecular function: RNA binding