SLC45A4

solute carrier family 45 member 4, the group of Solute carrier family 45

Basic information

Region (hg38): 8:141207166-141308305

Links

ENSG00000022567 ∙ NCBI:57210 ∙ OMIM:619581 ∙ HGNC:29196 ∙ Uniprot:Q5BKX6 ∙ 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 SLC45A4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC45A4 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				2	9	11
missense			109	9	3	121
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	109	11	13

Variants in SLC45A4

This is a list of pathogenic ClinVar variants found in the SLC45A4 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-141211495-C-T		not specified	Likely benign (Aug 13, 2021)
8-141211527-C-T		not specified	Uncertain significance (Jun 07, 2024)
8-141211529-C-A		not specified	Uncertain significance (Apr 26, 2023)
8-141211582-C-A		not specified	Uncertain significance (Aug 08, 2022)
8-141211585-A-G		not specified	Likely benign (Jan 25, 2023)
8-141211647-C-T		not specified	Uncertain significance (Sep 25, 2023)
8-141211648-G-A		not specified	Likely benign (Apr 12, 2024)
8-141211665-C-T		not specified	Uncertain significance (Oct 26, 2021)
8-141211671-C-G		not specified	Uncertain significance (Oct 25, 2024)
8-141211700-A-G			Benign (Mar 30, 2018)
8-141212205-C-G		not specified	Uncertain significance (Apr 28, 2022)
8-141212207-G-C		not specified	Uncertain significance (Feb 17, 2022)
8-141212216-G-A		not specified	Likely benign (Mar 07, 2024)
8-141212230-C-G			Benign (Mar 30, 2018)
8-141212232-C-T		not specified	Uncertain significance (Oct 18, 2021)
8-141212237-C-T		not specified	Uncertain significance (May 08, 2024)
8-141212239-C-T			Benign (Apr 16, 2018)
8-141212249-A-G		not specified	Uncertain significance (Jul 26, 2024)
8-141212291-C-T		not specified	Uncertain significance (Nov 29, 2024)
8-141212292-C-T		not specified	Likely benign (Mar 06, 2025)
8-141212309-A-G		not specified	Uncertain significance (Jul 02, 2024)
8-141212312-C-G		not specified	Uncertain significance (Apr 23, 2024)
8-141212333-T-G		not specified	Uncertain significance (Sep 18, 2024)
8-141212343-C-T		not specified	Uncertain significance (Oct 14, 2021)
8-141212393-C-T		not specified	Uncertain significance (Dec 24, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC45A4	protein_coding	protein_coding	ENST00000024061	8	101140

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000104	0.998	125724	0	24	125748	0.0000954

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.833	486	540	0.899	0.0000393	5137
Missense in Polyphen		119	158.76	0.74954		1527
Synonymous	-1.41	275	247	1.11	0.0000206	1655
Loss of Function	2.67	11	25.5	0.431	0.00000118	273

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000397	0.000395
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000546	0.0000544
Finnish	0.000139	0.000139
European (Non-Finnish)	0.0000797	0.0000791
Middle Eastern	0.0000546	0.0000544
South Asian	0.0000654	0.0000653
Other	0.000166	0.000163

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0935

Intolerance Scores

• loftool: 0.127
• rvis_EVS: -1.3
• rvis_percentile_EVS: 4.99

Haploinsufficiency Scores

• pHI: 0.252
• hipred: Y
• hipred_score: 0.510
• ghis: 0.484

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.808

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc45a4

Gene ontology

• Biological process: sucrose transport
• Cellular component: membrane;integral component of membrane
• Molecular function: sucrose:proton symporter activity