HNRNPUL2-BSCL2

HNRNPUL2-BSCL2 readthrough (NMD candidate)

Basic information

Region (hg38): 11:62690275-62727384

Links

ENSG00000234857 ∙ NCBI:100534595 ∙ ∙ HGNC:49189 ∙ ∙ ∙ 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 HNRNPUL2-BSCL2 gene.

• Charcot-Marie-Tooth disease type 2 (330 variants)
• not provided (149 variants)
• Inborn genetic diseases (100 variants)
• Congenital generalized lipodystrophy type 2 (75 variants)
• not specified (39 variants)
• Neuronopathy, distal hereditary motor, type 5A (38 variants)
• Berardinelli-Seip congenital lipodystrophy (34 variants)
• Hereditary spastic paraplegia (24 variants)
• Severe neurodegenerative syndrome with lipodystrophy (14 variants)
• Neuronopathy, distal hereditary motor, type 5C (12 variants)
• Monogenic diabetes (10 variants)
• Hereditary spastic paraplegia 17 (9 variants)
• Severe neurodegenerative syndrome with lipodystrophy;Congenital generalized lipodystrophy type 2;Hereditary spastic paraplegia 17;Neuronopathy, distal hereditary motor, type 5C (7 variants)
• Congenital generalized lipodystrophy type 2;Neuronopathy, distal hereditary motor, type 5C;Hereditary spastic paraplegia 17;Severe neurodegenerative syndrome with lipodystrophy (5 variants)
• Congenital generalized lipodystrophy type 2;Severe neurodegenerative syndrome with lipodystrophy;Hereditary spastic paraplegia 17;Neuronopathy, distal hereditary motor, type 5C (4 variants)
• Hereditary spastic paraplegia 17;Neuronopathy, distal hereditary motor, type 5C;Severe neurodegenerative syndrome with lipodystrophy;Congenital generalized lipodystrophy type 2 (4 variants)
• Severe neurodegenerative syndrome with lipodystrophy;Congenital generalized lipodystrophy type 2;Neuronopathy, distal hereditary motor, type 5C;Hereditary spastic paraplegia 17 (3 variants)
• Neuronopathy, distal hereditary motor, type 5C;Congenital generalized lipodystrophy type 2;Hereditary spastic paraplegia 17;Severe neurodegenerative syndrome with lipodystrophy (3 variants)
• See cases (2 variants)
• Charcot-Marie-Tooth disease (2 variants)
• Neuronopathy, distal hereditary motor, type 5C;Severe neurodegenerative syndrome with lipodystrophy;Congenital generalized lipodystrophy type 2;Hereditary spastic paraplegia 17 (2 variants)
• Hereditary spastic paraplegia 17;Severe neurodegenerative syndrome with lipodystrophy;Congenital generalized lipodystrophy type 2;Neuronopathy, distal hereditary motor, type 5C (2 variants)
• Neuronopathy, distal hereditary motor, type 5C;Severe neurodegenerative syndrome with lipodystrophy;Hereditary spastic paraplegia 17;Congenital generalized lipodystrophy type 2 (2 variants)
• HNRNPUL2-related condition (2 variants)
• Congenital generalized lipodystrophy type 2;Hereditary spastic paraplegia 17;Neuronopathy, distal hereditary motor, type 5C;Severe neurodegenerative syndrome with lipodystrophy (2 variants)
• Severe neurodegenerative syndrome with lipodystrophy;Neuronopathy, distal hereditary motor, type 5C;Congenital generalized lipodystrophy type 2;Hereditary spastic paraplegia 17 (2 variants)
• Congenital generalized lipodystrophy type 2;Neuronopathy, distal hereditary motor, type 5C;Severe neurodegenerative syndrome with lipodystrophy;Hereditary spastic paraplegia 17 (2 variants)
• Early infantile epileptic encephalopathy with suppression bursts (1 variants)
• Neuronopathy, distal hereditary motor, type 5A;Hereditary spastic paraplegia 17 (1 variants)
• BSCL2-related condition (1 variants)
• Neurologic Disorders/Seipinopathy (1 variants)
• Peripheral neuropathy (1 variants)
• Congenital generalized lipodystrophy type 2;Hereditary spastic paraplegia 17;Severe neurodegenerative syndrome with lipodystrophy;Neuronopathy, distal hereditary motor, type 5C (1 variants)
• Congenital generalized lipodystrophy (1 variants)
• Neutrophilia in presence of infection;Isolated systolic hypertension;Triangular shaped proximal phalanx of the thumb (1 variants)
• Breast carcinoma (1 variants)
• Neuronopathy, distal hereditary motor, type 5A;Severe neurodegenerative syndrome with lipodystrophy;Congenital generalized lipodystrophy type 2;Hereditary spastic paraplegia 17 (1 variants)
• Neuronopathy, distal hereditary motor, type 5C;Hereditary spastic paraplegia 17;Congenital generalized lipodystrophy type 2;Severe neurodegenerative syndrome with lipodystrophy (1 variants)
• BSCL2-related Developmental and epileptic encephalopathy (1 variants)
• Reduced delayed hypersensitivity (1 variants)
• Abnormal central motor function (1 variants)
• PPARG-related familial partial lipodystrophy (1 variants)
• Severe neurodegenerative syndrome with lipodystrophy;Neuronopathy, distal hereditary motor, type 5C;Hereditary spastic paraplegia 17;Congenital generalized lipodystrophy type 2 (1 variants)
• Congenital generalized lipodystrophy type 2;Severe neurodegenerative syndrome with lipodystrophy;Neuronopathy, distal hereditary motor, type 5C;Hereditary spastic paraplegia 17 (1 variants)
• Symphalangism affecting the proximal phalanx of the 4th finger (1 variants)
• Hereditary spastic paraplegia 17;Neuronopathy, distal hereditary motor, type 5C (1 variants)
• Severe neurodegenerative syndrome with lipodystrophy;Hereditary spastic paraplegia 17;Neuronopathy, distal hereditary motor, type 5C;Congenital generalized lipodystrophy type 2 (1 variants)
• Lipodystrophy (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HNRNPUL2-BSCL2 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						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)	4	9	28	22		63
splice region						0
non coding	22	10	232	161	18	443
Total	26	19	260	183	18

Highest pathogenic variant AF is 0.000269

Variants in HNRNPUL2-BSCL2

This is a list of pathogenic ClinVar variants found in the HNRNPUL2-BSCL2 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-62690309-C-T		Congenital generalized lipodystrophy type 2 • Neuronopathy, distal hereditary motor, type 5A	Uncertain significance (Jan 13, 2018)
11-62690318-A-C		Neuronopathy, distal hereditary motor, type 5A • Congenital generalized lipodystrophy type 2	Uncertain significance (Jan 12, 2018)
11-62690369-AGGAACTAGAGCAGGTGGGGCGCTGTC-A		Charcot-Marie-Tooth disease type 2	Pathogenic (Sep 25, 2023)
11-62690371-G-T		Neuronopathy, distal hereditary motor, type 5C;Severe neurodegenerative syndrome with lipodystrophy;Congenital generalized lipodystrophy type 2;Hereditary spastic paraplegia 17	Uncertain significance (Aug 02, 2021)
11-62690377-G-A			Uncertain significance (Jan 24, 2024)
11-62690380-C-G		Inborn genetic diseases	Uncertain significance (Feb 02, 2022)
11-62690380-C-T		Charcot-Marie-Tooth disease type 2	Uncertain significance (Sep 07, 2022)
11-62690382-G-A		Charcot-Marie-Tooth disease type 2	Likely benign (May 09, 2018)
11-62690383-G-A		Charcot-Marie-Tooth disease type 2	Uncertain significance (Sep 29, 2019)
11-62690385-G-T		Charcot-Marie-Tooth disease type 2	Likely benign (Mar 26, 2023)
11-62690387-G-A			Uncertain significance (Mar 01, 2017)
11-62690388-G-A		Charcot-Marie-Tooth disease type 2	Likely benign (Dec 13, 2020)
11-62690389-C-T		Monogenic diabetes • Charcot-Marie-Tooth disease type 2 • Hereditary spastic paraplegia • Congenital generalized lipodystrophy type 2 • Inborn genetic diseases	Conflicting classifications of pathogenicity (Dec 21, 2023)
11-62690395-C-A			Uncertain significance (Aug 22, 2016)
11-62690395-C-T		Charcot-Marie-Tooth disease type 2	Uncertain significance (Dec 19, 2023)
11-62690396-G-A		Severe neurodegenerative syndrome with lipodystrophy • Charcot-Marie-Tooth disease type 2	Conflicting classifications of pathogenicity (Feb 11, 2023)
11-62690397-G-C		Charcot-Marie-Tooth disease type 2	Likely benign (May 13, 2021)
11-62690402-C-A		Charcot-Marie-Tooth disease type 2 • BSCL2-related Developmental and epileptic encephalopathy • Inborn genetic diseases	Uncertain significance (Nov 05, 2023)
11-62690404-C-G		Charcot-Marie-Tooth disease type 2	Uncertain significance (Nov 17, 2023)
11-62690415-T-C		Charcot-Marie-Tooth disease type 2	Likely benign (Aug 21, 2022)
11-62690426-C-T		Charcot-Marie-Tooth disease type 2 • Inborn genetic diseases	Uncertain significance (Oct 08, 2021)
11-62690431-G-A			Uncertain significance (Dec 24, 2015)
11-62690436-T-C		Charcot-Marie-Tooth disease type 2	Likely benign (May 14, 2022)
11-62690439-G-T		PPARG-related familial partial lipodystrophy • Inborn genetic diseases	Likely benign (Jul 11, 2019)
11-62690441-C-T		Inborn genetic diseases	Uncertain significance (May 26, 2021)

GnomAD

Source: gnomAD

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• ghis: 0.419