HNRNPDL

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

Basic information

Region (hg38): 4:82422565-82430462

Previous symbols: [ "HNRPDL", "LGMD1G" ]

Links

ENSG00000152795 ∙ NCBI:9987 ∙ OMIM:607137 ∙ HGNC:5037 ∙ Uniprot:O14979 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• autosomal dominant limb-girdle muscular dystrophy type 1G (Strong), mode of inheritance: AD
• autosomal dominant limb-girdle muscular dystrophy type 1G (Supportive), mode of inheritance: AD
• muscular dystrophy, limb-girdle, autosomal dominant (Moderate), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Muscular dystrophy, limb-girdle, autosomal dominant 3	AD	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Musculoskeletal; Ophthalmologic	24647604

ClinVar

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

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HNRNPDL 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			5	105	5	115
missense		2	168		3	173
nonsense			2			2
start loss						0
frameshift			7			7
inframe indel			11	1		12
splice donor/acceptor (+/-2bp)						0
splice region			4	4	1	9
non coding			10	37	11	58
Total	0	2	203	143	19

Variants in HNRNPDL

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

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

Position	Type	Phenotype	Significance	ClinVar
4-82425953-T-C			Benign (May 16, 2021)
4-82426062-G-A		Autosomal dominant limb-girdle muscular dystrophy type 1G	Likely benign (Feb 09, 2023)
4-82426064-A-G			Uncertain significance (Jan 23, 2024)
4-82426071-G-A		Autosomal dominant limb-girdle muscular dystrophy type 1G	Likely benign (Mar 08, 2023)
4-82426074-A-G		Autosomal dominant limb-girdle muscular dystrophy type 1G	Likely benign (Nov 01, 2022)
4-82426083-G-A		Autosomal dominant limb-girdle muscular dystrophy type 1G	Likely benign (Nov 29, 2023)
4-82426085-GA-TT		Autosomal dominant limb-girdle muscular dystrophy type 1G	Uncertain significance (Feb 02, 2022)
4-82426113-A-G		Autosomal dominant limb-girdle muscular dystrophy type 1G	Benign (Jan 31, 2024)
4-82426119-G-A		Autosomal dominant limb-girdle muscular dystrophy type 1G	Likely benign (Nov 08, 2022)
4-82426124-G-C		Autosomal dominant limb-girdle muscular dystrophy type 1G	Uncertain significance (Oct 08, 2023)
4-82426133-T-C		Autosomal dominant limb-girdle muscular dystrophy type 1G	Uncertain significance (Jul 19, 2022)
4-82426138-A-G			Likely benign (Jul 12, 2018)
4-82426145-A-G		Autosomal dominant limb-girdle muscular dystrophy type 1G	Likely benign (Nov 28, 2022)
4-82426156-TAAGA-T			Benign (May 12, 2021)
4-82426445-T-A		Autosomal dominant limb-girdle muscular dystrophy type 1G	Likely benign (Oct 04, 2023)
4-82426450-T-TC		Autosomal dominant limb-girdle muscular dystrophy type 1G	Likely benign (Sep 09, 2022)
4-82426465-C-T		Autosomal dominant limb-girdle muscular dystrophy type 1G	Uncertain significance (Jul 25, 2022)
4-82426473-T-C		Autosomal dominant limb-girdle muscular dystrophy type 1G	Likely benign (Dec 19, 2023)
4-82426498-T-C			Uncertain significance (Oct 12, 2023)
4-82426500-C-A		Autosomal dominant limb-girdle muscular dystrophy type 1G	Uncertain significance (Oct 12, 2019)
4-82426513-C-A		Autosomal dominant limb-girdle muscular dystrophy type 1G	Uncertain significance (Jul 12, 2022)
4-82426519-T-C		Autosomal dominant limb-girdle muscular dystrophy type 1G	Uncertain significance (Jan 11, 2022)
4-82426523-C-G		Autosomal dominant limb-girdle muscular dystrophy type 1G • HNRNPDL-related myopathy with protein aggregates and rimmed vacuoles	Pathogenic/Likely pathogenic (Mar 01, 2024)
4-82426523-C-T		Autosomal dominant limb-girdle muscular dystrophy type 1G	Conflicting classifications of pathogenicity (Jun 27, 2023)
4-82426525-T-C		Autosomal dominant limb-girdle muscular dystrophy type 1G	Uncertain significance (Jul 29, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HNRNPDL	protein_coding	protein_coding	ENST00000295470	7	7578

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0780	0.922	125734	0	13	125747	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.701	182	211	0.864	0.00000961	2701
Missense in Polyphen		20	43.074	0.46432		603
Synonymous	-4.33	129	79.8	1.62	0.00000371	818
Loss of Function	3.09	6	21.4	0.280	0.00000110	253

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.0000994	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000991	0.0000879
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a transcriptional regulator. Promotes transcription repression. Promotes transcription activation in differentiated myotubes (By similarity). Binds to double- and single-stranded DNA sequences. Binds to the transcription suppressor CATR sequence of the COX5B promoter (By similarity). Binds with high affinity to RNA molecules that contain AU-rich elements (AREs) found within the 3'-UTR of many proto-oncogenes and cytokine mRNAs. Binds both to nuclear and cytoplasmic poly(A) mRNAs. Binds to poly(G) and poly(A), but not to poly(U) or poly(C) RNA homopolymers. Binds to the 5'-ACUAGC-3' RNA consensus sequence. {ECO:0000250, ECO:0000269|PubMed:9538234}.
• Disease: DISEASE: Limb-girdle muscular dystrophy 1G (LGMD1G) [MIM:609115]: An autosomal dominant degenerative myopathy characterized by slowly progressive wasting and weakness of the proximal muscles of arms and legs around the pelvic or shoulder girdles, elevated creatine kinase levels and dystrophic features on muscle biopsy. LGMD1G is characterized by a mild late-onset and is associated with progressive fingers and toes flexion limitation. Affected individuals may also develop cataracts before age 50. {ECO:0000269|PubMed:24647604}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation;EGFR1 (Consensus)

Recessive Scores

• pRec: 0.132

Intolerance Scores

• rvis_EVS: -0.25
• rvis_percentile_EVS: 35.75

Haploinsufficiency Scores

• pHI: 0.369
• hipred: Y
• hipred_score: 0.673
• ghis: 0.665

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hnrnpdl

Zebrafish Information Network

• Gene name: hnrnpdl
• Affected structure: muscle cell
• Phenotype tag: abnormal
• Phenotype quality: disorganized

Gene ontology

• Biological process: interleukin-12-mediated signaling pathway
• Cellular component: nucleus;nucleoplasm;cytosol;ribonucleoprotein complex
• Molecular function: RNA binding;protein binding;poly(A) binding;poly(G) binding;sequence-specific DNA binding;sequence-specific double-stranded DNA binding