SLC35B2

solute carrier family 35 member B2, the group of MicroRNA protein coding host genes|Solute carrier family 35

Basic information

Region (hg38): 6:44254095-44257890

Links

ENSG00000157593 ∙ NCBI:347734 ∙ OMIM:610788 ∙ HGNC:16872 ∙ Uniprot:Q8TB61 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• leukodystrophy, hypomyelinating, 26, with chondrodysplasia (Limited), mode of inheritance: AR
• leukodystrophy, hypomyelinating, 26, with chondrodysplasia (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Leukodystrophy, hypomyelinating, 26, with chondrodysplasia	AR	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; Neurologic	35325049

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC35B2 gene.

• Inborn genetic diseases (30 variants)
• not provided (3 variants)
• Leukodystrophy, hypomyelinating, 26, with chondrodysplasia (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC35B2 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				1	1	2
missense			29	1	1	31
nonsense						0
start loss						0
frameshift	1					1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	1	0	29	2	2

Highest pathogenic variant AF is 0.0000329

Variants in SLC35B2

This is a list of pathogenic ClinVar variants found in the SLC35B2 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-44254727-C-G		not specified	Uncertain significance (Aug 17, 2022)
6-44254753-G-A		not specified	Uncertain significance (Mar 04, 2024)
6-44254764-C-G		not specified	Uncertain significance (Sep 01, 2021)
6-44254770-C-T		not specified	Uncertain significance (Jan 05, 2022)
6-44254774-C-T		not specified	Uncertain significance (Apr 11, 2023)
6-44254779-ACT-A		Leukodystrophy, hypomyelinating, 26, with chondrodysplasia	Pathogenic (Apr 27, 2023)
6-44254784-GAGC-G		Primary bone dysplasia with multiple joint dislocations • Leukodystrophy, hypomyelinating, 26, with chondrodysplasia	Pathogenic (Feb 28, 2023)
6-44254794-G-C		not specified	Uncertain significance (Feb 10, 2022)
6-44254806-A-G		not specified	Uncertain significance (May 04, 2022)
6-44254888-G-A		not specified	Uncertain significance (Dec 28, 2023)
6-44254909-C-T		not specified	Uncertain significance (Sep 20, 2023)
6-44254920-A-T		not specified	Uncertain significance (Dec 21, 2023)
6-44254922-C-G		not specified	Uncertain significance (Oct 05, 2021)
6-44254933-T-C		not specified	Uncertain significance (May 05, 2023)
6-44254948-G-T		not specified	Uncertain significance (Jul 12, 2022)
6-44254981-G-C			Benign (Jul 20, 2018)
6-44255007-C-T		not specified	Uncertain significance (Nov 09, 2021)
6-44255109-G-A		not specified	Uncertain significance (Oct 22, 2021)
6-44255166-G-A		not specified	Uncertain significance (Apr 14, 2022)
6-44255214-G-A		not specified	Uncertain significance (Mar 01, 2023)
6-44255220-C-G		not specified	Uncertain significance (Dec 15, 2021)
6-44255221-G-A		not specified	Uncertain significance (Dec 21, 2022)
6-44255257-C-T		not specified	Uncertain significance (Jul 17, 2023)
6-44255299-C-T		not specified	Uncertain significance (Sep 28, 2022)
6-44255302-A-G		not specified	Uncertain significance (Feb 06, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC35B2	protein_coding	protein_coding	ENST00000393812	4	3459

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0715	0.926	125701	0	47	125748	0.000187

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.261	263	251	1.05	0.0000141	2748
Missense in Polyphen		72	81.672	0.88158		985
Synonymous	-2.37	137	106	1.29	0.00000574	961
Loss of Function	2.66	5	16.7	0.299	9.15e-7	162

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000173	0.000173
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.000693	0.000693
European (Non-Finnish)	0.000167	0.000167
Middle Eastern	0.000109	0.000109
South Asian	0.0000980	0.0000980
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Mediates the transport of adenosine 3'-phospho 5'- phosphosulfate (PAPS), from cytosol into Golgi. PAPS is a universal sulfuryl donor for sulfation events that take place in the Golgi. May indirectly participate in activation of the NF- kappa-B and MAPK pathways. {ECO:0000269|PubMed:12716889}.
• Pathway: Transport and synthesis of PAPS;Metabolism of carbohydrates;Phase II - Conjugation of compounds;Glycosaminoglycan metabolism;Biological oxidations;Metabolism;Transport of vitamins, nucleosides, and related molecules;SLC-mediated transmembrane transport;Transport of small molecules;Cytosolic sulfonation of small molecules;Methionine and cysteine metabolism;Transport of nucleotide sugars (Consensus)

Intolerance Scores

• loftool: 0.698
• rvis_EVS: -0.82
• rvis_percentile_EVS: 11.77

Haploinsufficiency Scores

• pHI: 0.245
• hipred: Y
• hipred_score: 0.595
• ghis: 0.588

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.911

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc35b2

Zebrafish Information Network

• Gene name: slc35b2
• Affected structure: retinal ganglion cell
• Phenotype tag: abnormal
• Phenotype quality: organization quality

Gene ontology

• Biological process: positive regulation of I-kappaB kinase/NF-kappaB signaling;3'-phosphoadenosine 5'-phosphosulfate transport;3'-phosphoadenosine 5'-phosphosulfate biosynthetic process;3'-phospho-5'-adenylyl sulfate transmembrane transport
• Cellular component: Golgi membrane;Golgi apparatus;membrane;integral component of membrane;integral component of Golgi membrane;integral component of endoplasmic reticulum membrane
• Molecular function: transmembrane transporter activity;3'-phosphoadenosine 5'-phosphosulfate transmembrane transporter activity