HNRNPA1L2

heterogeneous nuclear ribonucleoprotein A1 like 2, the group of Heterogeneous nuclear ribonucleoproteins|RNA binding motif containing

Basic information

Region (hg38): 13:52642431-52643773

Links

ENSG00000139675 ∙ NCBI:144983 ∙ ∙ HGNC:27067 ∙ Uniprot:Q32P51 ∙ 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 HNRNPA1L2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HNRNPA1L2 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						0
missense			25			25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	25	0	0

Variants in HNRNPA1L2

This is a list of pathogenic ClinVar variants found in the HNRNPA1L2 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-52642523-G-A		not specified	Uncertain significance (Oct 05, 2021)
13-52642538-C-T		not specified	Uncertain significance (Oct 24, 2024)
13-52642545-T-C		not specified	Uncertain significance (Dec 24, 2024)
13-52642593-T-C		not specified	Uncertain significance (Dec 29, 2024)
13-52642601-T-C		not specified	Uncertain significance (Feb 12, 2025)
13-52642603-G-T		not specified	Uncertain significance (Aug 09, 2021)
13-52642629-T-A		not specified	Uncertain significance (Oct 17, 2024)
13-52642640-A-G		not specified	Uncertain significance (Jun 17, 2022)
13-52642649-C-T		not specified	Uncertain significance (Apr 17, 2024)
13-52642650-G-A		not specified	Uncertain significance (May 09, 2023)
13-52642716-C-T		not specified	Uncertain significance (Jun 11, 2021)
13-52642829-A-G		not specified	Uncertain significance (Nov 10, 2022)
13-52642842-A-G		not specified	Uncertain significance (May 29, 2024)
13-52642885-T-G		not specified	Uncertain significance (Nov 09, 2023)
13-52642941-T-C		not specified	Uncertain significance (Jan 22, 2025)
13-52642955-G-A		not specified	Uncertain significance (Oct 07, 2024)
13-52642997-A-G		not specified	Uncertain significance (Jun 02, 2024)
13-52643051-G-A		not specified	Uncertain significance (Apr 15, 2024)
13-52643123-G-A		not specified	Uncertain significance (Oct 03, 2023)
13-52643124-G-A		not specified	Uncertain significance (Jan 27, 2025)
13-52643161-T-G		not specified	Uncertain significance (Dec 03, 2024)
13-52643165-C-T		not specified	Uncertain significance (Oct 07, 2024)
13-52643166-G-A		not specified	Uncertain significance (Dec 06, 2021)
13-52643196-G-A		not specified	Uncertain significance (Jul 20, 2021)
13-52643226-A-T		not specified	Uncertain significance (Jan 10, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HNRNPA1L2	protein_coding	protein_coding	ENST00000342657	1	26315

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0188	0.515	124138	8	1402	125548	0.00563

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0677	178	175	1.01	0.00000914	2110
Missense in Polyphen		30	34.028	0.88163		465
Synonymous	-0.460	69	64.3	1.07	0.00000360	622
Loss of Function	-0.363	2	1.52	1.32	6.41e-8	20

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0213	0.0207
Ashkenazi Jewish	0.00556	0.00557
East Asian	0.00	0.00
Finnish	0.00305	0.00305
European (Non-Finnish)	0.00310	0.00310
Middle Eastern	0.00	0.00
South Asian	0.0169	0.0168
Other	0.00510	0.00508

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in the packaging of pre-mRNA into hnRNP particles, transport of poly(A) mRNA from the nucleus to the cytoplasm and may modulate splice site selection. {ECO:0000250}.
• Pathway: Spliceosome - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.0731

Intolerance Scores

• loftool: 0.339
• rvis_EVS: 1.31
• rvis_percentile_EVS: 94

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.304
• ghis: 0.415

Essentials

• essential_gene_CRISPR: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.231

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hnrnpa1l2-ps2

Gene ontology

• Biological process: mRNA processing;RNA splicing;mRNA transport
• Cellular component: nucleus;spliceosomal complex;cytoplasm;ribonucleoprotein complex
• Molecular function: RNA binding;mRNA binding