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. These statistics are base on transcript: . Only rare variants are included in the table.

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				26 clinvar	1 clinvar	27
missense		1 clinvar	58 clinvar	4 clinvar	1 clinvar	64
nonsense		1 clinvar				1
start loss						0
frameshift	1 clinvar	1 clinvar	1 clinvar			3
splice donor/acceptor (+/-2bp)		1 clinvar				1
Total	1	4	59	30	2

Loading clinvar variants...

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