SLC41A2

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

Basic information

Region (hg38): 12:104801801-104958744

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_specified (57 variants)
• not_provided (4 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. These statistics are base on transcript: NM_001352171.3. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			56	1		57
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	56	1	0

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