SLC48A1

solute carrier family 48 member 1, the group of Solute carrier family 48

Basic information

Region (hg38): 12:47753916-47782751

Links

ENSG00000211584 ∙ NCBI:55652 ∙ OMIM:612187 ∙ HGNC:26035 ∙ Uniprot:Q6P1K1 ∙ 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 SLC48A1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC48A1 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			11			11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	0	0

Variants in SLC48A1

This is a list of pathogenic ClinVar variants found in the SLC48A1 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-47757871-G-A		not specified	Uncertain significance (Dec 21, 2023)
12-47757894-C-T		not specified	Uncertain significance (Dec 30, 2024)
12-47757921-G-A		not specified	Uncertain significance (Jan 22, 2025)
12-47757977-C-T			Benign (Aug 15, 2017)
12-47757978-G-A		not specified	Uncertain significance (Oct 01, 2024)
12-47757985-C-T		not specified	Uncertain significance (Jul 02, 2024)
12-47758005-C-G		not specified	Likely benign (Jul 15, 2021)
12-47758005-C-T		not specified	Likely benign (Aug 20, 2024)
12-47758017-A-G		not specified	Uncertain significance (Dec 28, 2022)
12-47758020-G-A		not specified	Uncertain significance (Jun 25, 2024)
12-47758070-C-A		not specified	Uncertain significance (Mar 07, 2023)
12-47773329-G-T		not specified	Uncertain significance (Oct 04, 2024)
12-47773347-T-C			Uncertain significance (Sep 12, 2022)
12-47773365-G-T		not specified	Uncertain significance (May 09, 2023)
12-47773386-G-C		not specified	Uncertain significance (Sep 27, 2021)
12-47773419-G-A		not specified	Uncertain significance (Aug 28, 2023)
12-47779126-G-A		not specified	Uncertain significance (Feb 01, 2025)
12-47779171-G-A		not specified	Uncertain significance (Dec 17, 2023)
12-47779178-C-T		not specified	Uncertain significance (Jan 01, 2025)
12-47779184-C-G		not specified	Uncertain significance (Jul 06, 2021)
12-47780159-A-G		not specified	Uncertain significance (Mar 31, 2023)
12-47780200-C-G		not specified	Uncertain significance (Jan 20, 2023)
12-47780226-A-G		not specified	Uncertain significance (Aug 13, 2021)
12-47780235-G-A		not specified	Uncertain significance (Feb 25, 2025)
12-47780258-A-G		not specified	Uncertain significance (Jan 09, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC48A1	protein_coding	protein_coding	ENST00000442218	3	28838

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.734	0.255	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.769	51	69.0	0.739	0.00000412	934
Missense in Polyphen		19	30.033	0.63264		342
Synonymous	-0.308	32	29.9	1.07	0.00000183	310
Loss of Function	1.94	0	4.38	0.00	1.89e-7	56

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Heme transporter that regulates intracellular heme availability through the endosomal or lysosomal compartment. {ECO:0000269|PubMed:18418376}.

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.336
• ghis: 0.495

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.258

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc48a1
• Phenotype: normal phenotype

Zebrafish Information Network

• Gene name: slc48a1b
• Affected structure: nucleate erythrocyte
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: heme transport
• Cellular component: lysosomal membrane;plasma membrane;endosome membrane;integral component of membrane
• Molecular function: protein binding;heme transporter activity;heme binding