SLC35A4

solute carrier family 35 member A4, the group of Solute carrier family 35

Basic information

Region (hg38): 5:140564445-140569100

Links

ENSG00000176087 ∙ NCBI:113829 ∙ OMIM:620297 ∙ HGNC:20753 ∙ Uniprot:L0R6Q1, Q96G79 ∙ 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 SLC35A4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC35A4 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			22	1		23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	1	0

Variants in SLC35A4

This is a list of pathogenic ClinVar variants found in the SLC35A4 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-140567299-G-A		not specified	Uncertain significance (Apr 27, 2022)
5-140567309-C-G		not specified	Uncertain significance (Oct 20, 2021)
5-140567321-C-T		not specified	Uncertain significance (Mar 07, 2023)
5-140567339-C-T		not specified	Uncertain significance (Oct 03, 2022)
5-140567362-T-C		not specified	Uncertain significance (Dec 22, 2023)
5-140567368-T-C		not specified	Uncertain significance (Mar 15, 2024)
5-140567420-G-A		not specified	Uncertain significance (Aug 17, 2021)
5-140567491-C-T		not specified	Uncertain significance (Jun 11, 2021)
5-140567572-C-T		not specified	Uncertain significance (Jun 02, 2024)
5-140567603-C-T		not specified	Uncertain significance (Aug 02, 2023)
5-140567617-A-C		not specified	Uncertain significance (Mar 08, 2024)
5-140567657-T-A		not specified	Likely benign (Aug 30, 2021)
5-140567663-G-A		not specified	Uncertain significance (Jun 29, 2022)
5-140567693-C-T		not specified	Uncertain significance (Aug 30, 2022)
5-140567743-C-G		not specified	Uncertain significance (Apr 07, 2022)
5-140567779-G-C		not specified	Uncertain significance (Dec 28, 2022)
5-140567804-G-A		not specified	Uncertain significance (Aug 21, 2023)
5-140567810-G-A		not specified	Uncertain significance (May 29, 2024)
5-140567881-G-A		not specified	Uncertain significance (Dec 07, 2021)
5-140567881-G-T		not specified	Uncertain significance (Oct 20, 2023)
5-140567891-C-T		not specified	Uncertain significance (Jun 12, 2023)
5-140567893-G-C		not specified	Uncertain significance (Mar 03, 2022)
5-140567965-C-T		not specified	Uncertain significance (Dec 16, 2023)
5-140568008-T-G		not specified	Uncertain significance (Jan 09, 2024)
5-140568026-C-T		not specified	Uncertain significance (Jun 07, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC35A4	protein_coding	protein_coding	ENST00000514199	1	4648

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000887	0.565	125707	0	41	125748	0.000163

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.147	202	196	1.03	0.0000125	2003
Missense in Polyphen		70	72.364	0.96733		870
Synonymous	-0.817	102	92.0	1.11	0.00000554	804
Loss of Function	0.616	7	8.99	0.778	5.58e-7	83

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000565	0.000564
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000272	0.000272
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000132	0.000132
Middle Eastern	0.000272	0.000272
South Asian	0.0000653	0.0000653
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.103

Intolerance Scores

• loftool: 0.685
• rvis_EVS: 0.37
• rvis_percentile_EVS: 75.29

Haploinsufficiency Scores

• pHI: 0.269
• hipred: N
• hipred_score: 0.256
• ghis: 0.485

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.517

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc35a4

Gene ontology

• Biological process: carbohydrate transport;sialic acid transport;pyrimidine nucleotide-sugar transmembrane transport
• Cellular component: Golgi apparatus;integral component of Golgi membrane
• Molecular function: sialic acid transmembrane transporter activity;pyrimidine nucleotide-sugar transmembrane transporter activity