SLC35D1

solute carrier family 35 member D1, the group of Solute carrier family 35

Basic information

Region (hg38): 1:66999350-67054148

Links

ENSG00000116704 ∙ NCBI:23169 ∙ OMIM:610804 ∙ HGNC:20800 ∙ Uniprot:Q9NTN3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• schneckenbecken dysplasia (Definitive), mode of inheritance: AR
• schneckenbecken dysplasia (Strong), mode of inheritance: AR
• schneckenbecken dysplasia (Supportive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Schneckenbecken dysplasia	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	11200994; 17952091; 19508970

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC35D1 gene.

• Schneckenbecken dysplasia (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC35D1 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	25	1	27
missense		1	50	4	1	56
nonsense		1				1
start loss						0
frameshift	1	1	1			3
inframe indel			1			1
splice donor/acceptor (+/-2bp)		1				1
splice region			4	10	3	17
non coding				37	39	76
Total	1	4	53	66	41

Variants in SLC35D1

This is a list of pathogenic ClinVar variants found in the SLC35D1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-67004361-A-G		Schneckenbecken dysplasia	Likely benign (May 25, 2022)
1-67004380-G-A		Inborn genetic diseases	Uncertain significance (Apr 23, 2024)
1-67004395-C-T		Inborn genetic diseases	Uncertain significance (May 30, 2024)
1-67004401-T-G		Schneckenbecken dysplasia	Likely benign (Dec 06, 2023)
1-67004422-T-C		Inborn genetic diseases	Uncertain significance (Apr 10, 2023)
1-67004432-C-A		Schneckenbecken dysplasia	Uncertain significance (Aug 22, 2022)
1-67004457-C-G		Schneckenbecken dysplasia • SLC35D1-related disorder	Likely benign (Aug 24, 2023)
1-67004526-T-C			Likely benign (Sep 01, 2018)
1-67008820-C-T			Benign (Jul 27, 2018)
1-67008840-TCAAG-T			Likely benign (Jul 10, 2019)
1-67009073-ATTT-A		Schneckenbecken dysplasia	Likely benign (Aug 31, 2022)
1-67009078-T-C		Schneckenbecken dysplasia	Likely benign (Feb 03, 2023)
1-67009089-T-C		Schneckenbecken dysplasia	Uncertain significance (Apr 25, 2022)
1-67009096-A-G		Schneckenbecken dysplasia	Likely benign (Nov 29, 2023)
1-67009099-A-T		Schneckenbecken dysplasia	Uncertain significance (Dec 17, 2020)
1-67009112-C-T		Schneckenbecken dysplasia	Pathogenic (Nov 01, 2007)
1-67009114-C-T		Connective tissue disorder • Schneckenbecken dysplasia	Conflicting classifications of pathogenicity (Nov 24, 2022)
1-67009117-G-A		Schneckenbecken dysplasia	Likely benign (Nov 01, 2023)
1-67009125-A-T		Schneckenbecken dysplasia	Likely pathogenic (Feb 06, 2021)
1-67009141-C-T		Inborn genetic diseases	Uncertain significance (May 13, 2024)
1-67009142-A-G		Schneckenbecken dysplasia	Uncertain significance (May 27, 2021)
1-67009151-TAA-T		Schneckenbecken dysplasia	Uncertain significance (Sep 01, 2021)
1-67009152-A-G		Schneckenbecken dysplasia	Uncertain significance (Aug 22, 2022)
1-67009181-T-C		Schneckenbecken dysplasia	Likely benign (Nov 02, 2023)
1-67009184-T-C		Schneckenbecken dysplasia	Likely benign (Oct 18, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC35D1	protein_coding	protein_coding	ENST00000235345	12	54768

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000355	0.990	125720	0	28	125748	0.000111

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0255	186	187	0.995	0.00000896	2287
Missense in Polyphen		53	67.849	0.78115		873
Synonymous	-1.75	96	76.5	1.25	0.00000409	726
Loss of Function	2.28	9	20.0	0.449	9.00e-7	249

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000241	0.000241
Ashkenazi Jewish	0.00	0.00
East Asian	0.000390	0.000381
Finnish	0.0000925	0.0000924
European (Non-Finnish)	0.0000645	0.0000615
Middle Eastern	0.000390	0.000381
South Asian	0.000200	0.000196
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transports both UDP-glucuronic acid (UDP-GlcA) and UDP- N-acetylgalactosamine (UDP-GalNAc) from the cytoplasm into the endoplasmic reticulum lumen (PubMed:11322953, PubMed:17952091). Plays a role in chondroitin sulfate biosynthesis, which is important for formation of cartilage extracellular matrix and normal skeletal development (By similarity). {ECO:0000250|UniProtKB:A2AKQ0, ECO:0000269|PubMed:11322953, ECO:0000269|PubMed:17952091}.
• Pathway: Formation of the active cofactor, UDP-glucuronate;Glucuronidation;Phase II - Conjugation of compounds;Biological oxidations;Metabolism;Transport of vitamins, nucleosides, and related molecules;SLC-mediated transmembrane transport;Transport of small molecules;O-Glycan biosynthesis;Transport of nucleotide sugars (Consensus)

Intolerance Scores

• loftool: 0.704
• rvis_EVS: -0.27
• rvis_percentile_EVS: 34.32

Haploinsufficiency Scores

• pHI: 0.358
• hipred: N
• hipred_score: 0.301
• ghis: 0.541

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.508

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc35d1
• Phenotype: skeleton phenotype; limbs/digits/tail phenotype; digestive/alimentary phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); craniofacial phenotype; growth/size/body region phenotype

Zebrafish Information Network

• Gene name: slc35d1a
• Affected structure: cartilage element
• Phenotype tag: abnormal
• Phenotype quality: morphology

Gene ontology

• Biological process: UDP-glucuronate biosynthetic process;carbohydrate transport;UDP-glucuronic acid transmembrane transport;chondroitin sulfate biosynthetic process;embryonic skeletal system development
• Cellular component: endoplasmic reticulum membrane;Golgi apparatus;integral component of membrane
• Molecular function: UDP-glucuronic acid transmembrane transporter activity;UDP-N-acetylglucosamine transmembrane transporter activity;UDP-N-acetylgalactosamine transmembrane transporter activity;pyrimidine nucleotide-sugar transmembrane transporter activity;antiporter activity;transmembrane transporter activity