SLC45A3

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

Basic information

Region (hg38): 1:205657851-205680509

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.

• not_specified (63 variants)
• not_provided (3 variants)
• Teratoma (1 variants)

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. These statistics are base on transcript: NM_000033102.3. 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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			63	4		67
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	63	4	0

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