SLC41A1

solute carrier family 41 member 1, the group of Solute carrier family 41

Basic information

Region (hg38): 1:205789093-205813748

Links

ENSG00000133065 ∙ NCBI:254428 ∙ OMIM:610801 ∙ HGNC:19429 ∙ Uniprot:Q8IVJ1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• nephronophthisis-like nephropathy 2 (Limited), mode of inheritance: Unknown
• kidney disorder (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Nephronophthisis-like nephropathy 2	AR	Allergy/Immunology/Infectious	Individuals have been described with frequent respiratory infections (including with Pseudomonas aeruginosa in one reported individual), and awareness of infectious risk may allow preventive management as well as prompt and aggressive treatment	Allergy/Immunology/Infectious; Renal	23661805
Renal transplantation has been described

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC41A1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC41A1 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				16	5	21
missense			40	1		41
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1	3		4
non coding				3	6	9
Total	0	0	40	20	11

Variants in SLC41A1

This is a list of pathogenic ClinVar variants found in the SLC41A1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-205791549-G-A			Uncertain significance (Apr 09, 2023)
1-205791555-C-T		not specified	Uncertain significance (Mar 01, 2023)
1-205791610-G-C		not specified	Uncertain significance (Oct 27, 2023)
1-205791624-G-A		not specified	Uncertain significance (May 02, 2024)
1-205791632-G-A			Likely benign (Aug 17, 2022)
1-205791704-C-T			Benign (Jan 25, 2024)
1-205791705-A-C		not specified	Uncertain significance (Dec 12, 2023)
1-205791709-G-C		not specified	Uncertain significance (Oct 02, 2023)
1-205791712-T-C		not specified	Uncertain significance (Nov 12, 2021)
1-205791722-G-C			Likely benign (Dec 21, 2023)
1-205794886-G-A		not specified	Uncertain significance (Dec 08, 2023)
1-205794897-G-T			Likely benign (Nov 23, 2022)
1-205794903-G-A			Benign (Dec 22, 2023)
1-205794980-C-T		not specified	Uncertain significance (Nov 18, 2022)
1-205794994-A-G		not specified	Uncertain significance (Aug 08, 2023)
1-205795305-A-C			Benign (May 17, 2021)
1-205795329-G-A			Benign (Oct 13, 2023)
1-205795339-G-A			Uncertain significance (Oct 04, 2023)
1-205795356-A-T		not specified	Uncertain significance (Sep 25, 2023)
1-205795379-C-T		not specified	Uncertain significance (Dec 20, 2023)
1-205795383-G-A			Uncertain significance (Jan 03, 2023)
1-205795390-T-C		Nephronophthisis-like nephropathy 2	Benign/Likely benign (Jan 23, 2024)
1-205795494-C-T			Likely benign (Jul 11, 2022)
1-205795495-G-C			Likely benign (Nov 22, 2022)
1-205795512-G-A			Benign (Nov 12, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC41A1	protein_coding	protein_coding	ENST00000367137	10	24656

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.655	0.345	125743	0	5	125748	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.48	225	297	0.758	0.0000187	3317
Missense in Polyphen		59	115.46	0.51101		1359
Synonymous	-0.603	134	125	1.07	0.00000865	1124
Loss of Function	3.43	4	20.9	0.191	0.00000119	215

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000264	0.0000264
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000335	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a magnesium transporter that is responsive to magnesium balance. {ECO:0000269|PubMed:15713785}.
• Pathway: Transport of bile salts and organic acids, metal ions and amine compounds;SLC-mediated transmembrane transport;Transport of small molecules;Metal ion SLC transporters (Consensus)

Recessive Scores

• pRec: 0.118

Intolerance Scores

• loftool: 0.291
• rvis_EVS: -0.98
• rvis_percentile_EVS: 8.75

Haploinsufficiency Scores

• pHI: 0.425
• hipred: Y
• hipred_score: 0.728
• ghis: 0.552

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0464

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc41a1

Zebrafish Information Network

• Gene name: slc41a1
• Affected structure: trunk
• Phenotype tag: abnormal
• Phenotype quality: curved ventral

Gene ontology

• Biological process: cellular magnesium ion homeostasis;magnesium ion transport;sodium ion transmembrane transport;divalent metal ion transport;cellular response to magnesium ion;magnesium ion transmembrane transport
• Cellular component: plasma membrane;integral component of membrane;basolateral plasma membrane;protein-containing complex
• Molecular function: magnesium ion transmembrane transporter activity;transmembrane transporter activity;magnesium:sodium antiporter activity;divalent inorganic cation transmembrane transporter activity