SLC35D3

solute carrier family 35 member D3, the group of Solute carrier family 35

Basic information

Region (hg38): 6:136922301-136925660

Previous symbols: [ "FRCL1" ]

Links

ENSG00000182747 ∙ NCBI:340146 ∙ OMIM:612519 ∙ HGNC:15621 ∙ Uniprot:Q5M8T2 ∙ AlphaFold ∙ 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 SLC35D3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC35D3 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
missense			27		1	28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	27	0	2

Variants in SLC35D3

This is a list of pathogenic ClinVar variants found in the SLC35D3 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-136922469-T-C		not specified	Uncertain significance (May 12, 2024)
6-136922476-C-G		not specified	Uncertain significance (Dec 19, 2022)
6-136922499-C-T		not specified	Uncertain significance (Aug 12, 2021)
6-136922576-T-C		not specified	Uncertain significance (Aug 26, 2024)
6-136922624-G-T		not specified	Uncertain significance (Sep 16, 2021)
6-136922636-T-C		not specified	Uncertain significance (Dec 23, 2024)
6-136922643-T-G		not specified	Uncertain significance (Mar 12, 2024)
6-136922647-C-A		not specified	Uncertain significance (Sep 12, 2024)
6-136922655-G-A		not specified	Uncertain significance (Dec 02, 2024)
6-136922775-T-C		not specified	Uncertain significance (Oct 25, 2024)
6-136922792-G-C		not specified	Uncertain significance (Nov 02, 2021)
6-136922855-G-A		not specified	Uncertain significance (Dec 21, 2022)
6-136923893-G-T		not specified	Uncertain significance (Oct 03, 2022)
6-136923948-A-G		not specified	Uncertain significance (Feb 23, 2023)
6-136923950-G-T		not specified	Uncertain significance (Aug 20, 2024)
6-136923999-G-A		not specified	Uncertain significance (Oct 05, 2022)
6-136924092-C-A		not specified	Uncertain significance (Nov 15, 2023)
6-136924121-G-T		not specified	Uncertain significance (Nov 25, 2024)
6-136924186-C-G			Benign (Aug 14, 2019)
6-136924226-G-C		not specified	Uncertain significance (Oct 25, 2022)
6-136924280-C-A		not specified	Uncertain significance (Sep 29, 2022)
6-136924355-G-C		not specified	Uncertain significance (Dec 15, 2021)
6-136924379-G-A		not specified	Uncertain significance (May 09, 2022)
6-136924429-C-A			Benign (Feb 08, 2018)
6-136924437-C-T		not specified	Uncertain significance (Apr 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC35D3	protein_coding	protein_coding	ENST00000331858	2	3376

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0361	0.932	125736	0	11	125747	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.07	216	265	0.814	0.0000152	2622
Missense in Polyphen		72	113.48	0.6345		1120
Synonymous	-0.409	137	131	1.05	0.00000907	924
Loss of Function	1.86	4	10.5	0.381	5.34e-7	110

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000120	0.000119
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000442	0.0000439
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in hemostasis as a regulator of the biosynthesis of platelet-dense granules. {ECO:0000250}.

Recessive Scores

• pRec: 0.114

Intolerance Scores

• rvis_EVS: 0.4
• rvis_percentile_EVS: 76.15

Haploinsufficiency Scores

• pHI: 0.394
• hipred: Y
• hipred_score: 0.651
• ghis: 0.401

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.138

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc35d3
• Phenotype: hematopoietic system phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: carbohydrate transport;positive regulation of protein exit from endoplasmic reticulum;energy homeostasis
• Cellular component: early endosome;endoplasmic reticulum;Golgi apparatus;integral component of membrane
• Molecular function: antiporter activity;transmembrane transporter activity