SLC41A2

solute carrier family 41 member 2, the group of Solute carrier family 41

Basic information

Region (hg38): 12:104801800-104958744

Links

ENSG00000136052 ∙ NCBI:84102 ∙ OMIM:610802 ∙ HGNC:31045 ∙ Uniprot:Q96JW4 ∙ 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 SLC41A2 gene.

• not provided (24 variants)
• Inborn genetic diseases (20 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC41A2 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	2
missense			20			20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					22	22
Total	0	0	20	0	24

Variants in SLC41A2

This is a list of pathogenic ClinVar variants found in the SLC41A2 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-104805069-G-A			Benign (May 15, 2021)
12-104805175-G-C		not specified	Uncertain significance (Apr 20, 2023)
12-104805260-G-A			Benign (May 04, 2021)
12-104805316-C-T		not specified	Uncertain significance (May 23, 2023)
12-104844552-T-C		not specified	Uncertain significance (Dec 21, 2022)
12-104845875-C-T		not specified	Uncertain significance (Jan 09, 2024)
12-104845932-G-A		not specified	Uncertain significance (Aug 09, 2021)
12-104846170-A-C			Benign (May 15, 2021)
12-104861325-C-G		not specified	Uncertain significance (Mar 31, 2023)
12-104861333-G-A		not specified	Uncertain significance (Aug 10, 2021)
12-104861333-G-C		not specified	Uncertain significance (Nov 09, 2021)
12-104866367-AAGAC-A			Benign (May 15, 2021)
12-104866380-GTACA-G			Benign (May 15, 2021)
12-104866381-TAC-T			Benign (May 16, 2021)
12-104866381-TACAC-T			Benign (May 18, 2021)
12-104866381-TACACAC-T			Benign (May 15, 2021)
12-104866381-TACACACAC-T			Benign (May 19, 2021)
12-104866415-CAT-C			Benign (May 20, 2021)
12-104866454-T-C		not specified	Uncertain significance (Oct 26, 2022)
12-104866587-TA-T			Benign (May 04, 2021)
12-104866587-TAA-T			Benign (May 04, 2021)
12-104866587-TAAA-T			Benign (May 04, 2021)
12-104866737-A-C			Benign (May 15, 2021)
12-104886079-AT-A			Benign (May 15, 2021)
12-104886153-C-A			Benign (May 15, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC41A2	protein_coding	protein_coding	ENST00000258538	10	156192

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.966	0.0340	125727	0	16	125743	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.78	207	293	0.707	0.0000135	3740
Missense in Polyphen		52	98.313	0.52893		1279
Synonymous	1.70	83	105	0.789	0.00000531	1131
Loss of Function	3.94	3	23.7	0.126	0.00000100	325

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000761	0.0000761
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000106	0.000105
Middle Eastern	0.00	0.00
South Asian	0.0000657	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a plasma-membrane magnesium transporter. {ECO:0000269|PubMed:16984228}.
• 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: 0.109

Intolerance Scores

• loftool: 0.336
• rvis_EVS: -0.16
• rvis_percentile_EVS: 41.64

Haploinsufficiency Scores

• pHI: 0.134
• hipred: Y
• hipred_score: 0.728
• ghis: 0.539

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.472

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc41a2

Gene ontology

• Biological process: magnesium ion transmembrane transport
• Cellular component: plasma membrane;integral component of membrane
• Molecular function: protein binding;magnesium ion transmembrane transporter activity;divalent inorganic cation transmembrane transporter activity