SLC45A3

solute carrier family 45 member 3, the group of Solute carrier family 45

Basic information

Region (hg38): 1:205657850-205680509

Previous symbols: [ "PCANAP6", "PCANAP2", "PCANAP8" ]

Links

ENSG00000158715 ∙ NCBI:85414 ∙ OMIM:605097 ∙ HGNC:8642 ∙ Uniprot:Q96JT2 ∙ 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 SLC45A3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC45A3 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			26	4		30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	4	0

Variants in SLC45A3

This is a list of pathogenic ClinVar variants found in the SLC45A3 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-205659259-C-T		not specified	Uncertain significance (Oct 12, 2021)
1-205659284-C-T		not specified	Uncertain significance (Apr 23, 2024)
1-205659314-C-T			Likely benign (Apr 01, 2024)
1-205659440-G-A		not specified	Uncertain significance (Jan 20, 2023)
1-205659445-G-A		not specified	Uncertain significance (Aug 02, 2021)
1-205659461-C-T		not specified	Uncertain significance (Apr 25, 2023)
1-205659484-C-T		Teratoma	Uncertain significance (Jan 01, 2023)
1-205659488-C-T			Likely benign (Mar 01, 2023)
1-205659520-G-A		not specified	Uncertain significance (Jul 06, 2021)
1-205659548-C-T		not specified	Uncertain significance (Oct 26, 2021)
1-205659550-C-T		not specified	Uncertain significance (Feb 21, 2024)
1-205659590-T-C		not specified	Uncertain significance (Jan 22, 2024)
1-205659592-G-C		not specified	Uncertain significance (May 17, 2023)
1-205659671-C-T		not specified	Uncertain significance (Feb 07, 2023)
1-205662054-C-T		not specified	Uncertain significance (Oct 17, 2023)
1-205662124-C-T		not specified	Uncertain significance (Jun 17, 2024)
1-205662844-T-G		not specified	Uncertain significance (Mar 20, 2024)
1-205662865-G-A		not specified	Likely benign (Mar 24, 2023)
1-205662994-C-T		not specified	Uncertain significance (Jun 29, 2023)
1-205663015-C-T		not specified	Uncertain significance (Dec 06, 2021)
1-205663016-G-A		not specified	Uncertain significance (Apr 13, 2023)
1-205663028-C-T		not specified	Uncertain significance (Jan 31, 2022)
1-205663031-C-A		not specified	Uncertain significance (Nov 18, 2022)
1-205663080-C-A		not specified	Uncertain significance (Jan 23, 2024)
1-205663112-C-T		not specified	Uncertain significance (Apr 25, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC45A3	protein_coding	protein_coding	ENST00000367145	4	22609

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00527	0.972	125718	0	30	125748	0.000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.58	268	351	0.763	0.0000224	3453
Missense in Polyphen		73	108.99	0.66979		1150
Synonymous	1.21	142	161	0.879	0.00000988	1315
Loss of Function	1.99	6	14.1	0.427	6.64e-7	156

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000311	0.000301
Ashkenazi Jewish	0.000202	0.0000992
East Asian	0.000495	0.000489
Finnish	0.00	0.00
European (Non-Finnish)	0.000134	0.0000879
Middle Eastern	0.000495	0.000489
South Asian	0.0000655	0.0000653
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Pathway: MicroRNAs in cancer - Homo sapiens (human);Transcriptional misregulation in cancer - Homo sapiens (human);SLC-mediated transmembrane transport;Transport of small molecules;Cellular hexose transport (Consensus)

Recessive Scores

• pRec: 0.133

Intolerance Scores

• loftool: 0.298
• rvis_EVS: -0.53
• rvis_percentile_EVS: 20.78

Haploinsufficiency Scores

• pHI: 0.630
• hipred: N
• hipred_score: 0.429
• ghis: 0.439

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.506

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc45a3

Gene ontology

• Biological process: hexose transmembrane transport;positive regulation of glucose metabolic process;sucrose transport;positive regulation of fatty acid biosynthetic process;regulation of oligodendrocyte differentiation
• Cellular component: plasma membrane;membrane;integral component of membrane
• Molecular function: sucrose:proton symporter activity;sugar transmembrane transporter activity