SLC45A1

solute carrier family 45 member 1, the group of Solute carrier family 45

Basic information

Region (hg38): 1:8318114-8344167

Previous symbols: [ "DNB5" ]

Links

ENSG00000162426 ∙ NCBI:50651 ∙ OMIM:605763 ∙ HGNC:17939 ∙ Uniprot:Q9Y2W3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• intellectual developmental disorder with neuropsychiatric features (Limited), mode of inheritance: AR
• autosomal recessive non-syndromic intellectual disability (Supportive), mode of inheritance: AR
• intellectual developmental disorder with neuropsychiatric features (Strong), mode of inheritance: AR
• intellectual developmental disorder with neuropsychiatric features (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Intellectual developmental disorder with neuropsychiatric features (IDDNPF)	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Craniofacial; Neurologic	27431290; 28434495

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC45A1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC45A1 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				33	9	42
missense		1	88	6	1	96
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region				1		1
non coding				1	1	2
Total	0	1	89	40	11

Variants in SLC45A1

This is a list of pathogenic ClinVar variants found in the SLC45A1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-8318130-C-T		SLC45A1-related disorder	Likely benign (May 21, 2019)
1-8318168-C-G			Benign/Likely benign (Jun 01, 2022)
1-8324338-C-T		SLC45A1-related disorder	Likely benign (Jan 13, 2020)
1-8324339-G-A		not specified	Uncertain significance (Dec 16, 2024)
1-8324355-C-T		not specified	Uncertain significance (Dec 02, 2022)
1-8324374-C-G			Uncertain significance (Nov 27, 2023)
1-8324381-G-A		SLC45A1-related disorder	Uncertain significance (Jan 12, 2023)
1-8324412-T-A		not specified	Uncertain significance (Jan 10, 2025)
1-8324415-C-T		not specified • Intellectual developmental disorder with neuropsychiatric features	Uncertain significance (Jun 22, 2023)
1-8324418-G-A			Uncertain significance (Jun 24, 2024)
1-8324439-G-T		Intellectual developmental disorder with neuropsychiatric features	Uncertain significance (Nov 18, 2019)
1-8324443-C-A		Intellectual developmental disorder with neuropsychiatric features	Uncertain significance (Jul 21, 2022)
1-8324453-C-T		not specified • Intellectual developmental disorder with neuropsychiatric features	Uncertain significance (May 16, 2024)
1-8324469-A-C		not specified	Uncertain significance (Nov 03, 2022)
1-8324498-C-T		not specified	Uncertain significance (Oct 09, 2024)
1-8324499-G-A		Intellectual developmental disorder with neuropsychiatric features	Uncertain significance (Jun 22, 2023)
1-8324505-C-G		not specified	Uncertain significance (Feb 10, 2025)
1-8324506-C-T		SLC45A1-related disorder	Likely benign (Mar 25, 2019)
1-8324509-A-C			Likely benign (Nov 01, 2022)
1-8324515-G-C		SLC45A1-related disorder	Likely benign (May 07, 2019)
1-8324530-G-C			Likely benign (May 01, 2023)
1-8324578-C-T			Likely benign (Oct 01, 2023)
1-8324600-G-A		not specified	Uncertain significance (Mar 05, 2024)
1-8324605-C-T			Likely benign (Jun 22, 2018)
1-8324676-G-T		not specified	Uncertain significance (Feb 13, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC45A1	protein_coding	protein_coding	ENST00000471889	8	26342

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000248	0.996	125647	0	101	125748	0.000402

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.47	408	500	0.816	0.0000351	4808
Missense in Polyphen		151	214.42	0.70422		2191
Synonymous	-0.321	249	243	1.03	0.0000202	1625
Loss of Function	2.56	12	26.1	0.460	0.00000139	272

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00131	0.00129
Ashkenazi Jewish	0.000102	0.0000992
East Asian	0.000384	0.000381
Finnish	0.000995	0.000971
European (Non-Finnish)	0.000412	0.000404
Middle Eastern	0.000384	0.000381
South Asian	0.00	0.00
Other	0.000664	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Proton-associated glucose transporter in the brain. {ECO:0000250|UniProtKB:Q8K4S3, ECO:0000269|PubMed:28434495}.

Recessive Scores

• pRec: 0.116

Intolerance Scores

• loftool: 0.184
• rvis_EVS: -2.04
• rvis_percentile_EVS: 1.67

Haploinsufficiency Scores

• pHI: 0.305
• hipred: Y
• hipred_score: 0.614
• ghis: 0.620

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.254

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc45a1

Gene ontology

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