SLC41A3

solute carrier family 41 member 3, the group of Solute carrier family 41

Basic information

Region (hg38): 3:126006357-126101561

Links

ENSG00000114544 ∙ NCBI:54946 ∙ OMIM:610803 ∙ HGNC:31046 ∙ Uniprot:Q96GZ6 ∙ 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 SLC41A3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC41A3 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					1	1
missense			26	2	1	29
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					12	12
Total	0	0	26	2	14

Variants in SLC41A3

This is a list of pathogenic ClinVar variants found in the SLC41A3 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-126006423-G-C		not specified	Uncertain significance (Sep 26, 2023)
3-126006455-C-A		not specified	Uncertain significance (Jan 04, 2022)
3-126006463-C-T		not specified	Uncertain significance (Apr 12, 2023)
3-126006498-A-C		not specified	Uncertain significance (Jun 07, 2024)
3-126006524-C-A		not specified	Uncertain significance (Dec 17, 2023)
3-126006809-C-T			Benign (Jun 19, 2021)
3-126007149-C-T		not specified	Uncertain significance (Sep 23, 2023)
3-126007188-C-T		not specified	Uncertain significance (Aug 28, 2024)
3-126007189-G-A		not specified	Uncertain significance (May 05, 2022)
3-126007205-G-C			Benign (Jun 09, 2021)
3-126008772-T-A		not specified	Uncertain significance (Dec 26, 2023)
3-126008826-A-T		not specified	Uncertain significance (Jun 28, 2022)
3-126008867-C-T		not specified	Uncertain significance (Jul 26, 2022)
3-126008877-A-G		not specified	Uncertain significance (Feb 22, 2023)
3-126012318-C-T			Benign (Jun 19, 2021)
3-126012675-C-T		not specified	Uncertain significance (Nov 08, 2024)
3-126012692-A-G		not specified	Uncertain significance (Aug 12, 2021)
3-126012726-T-G		not specified	Uncertain significance (Jan 10, 2023)
3-126012728-G-C		not specified	Uncertain significance (Apr 20, 2024)
3-126015496-C-T		not specified	Uncertain significance (Sep 12, 2023)
3-126015498-T-C		not specified	Uncertain significance (Sep 02, 2024)
3-126015503-C-T		not specified	Likely benign (Jul 14, 2024)
3-126015545-C-T		not specified	Likely benign (Feb 07, 2023)
3-126016747-C-T		not specified	Uncertain significance (Aug 01, 2022)
3-126016756-T-C		not specified	Uncertain significance (Oct 24, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC41A3	protein_coding	protein_coding	ENST00000315891	11	95207

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.07e-13	0.0616	125694	0	54	125748	0.000215

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.594	253	281	0.900	0.0000147	3216
Missense in Polyphen		91	98.006	0.92852		1165
Synonymous	0.868	108	120	0.899	0.00000686	1093
Loss of Function	0.479	21	23.5	0.893	0.00000128	241

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000299	0.000299
Ashkenazi Jewish	0.00	0.00
East Asian	0.000278	0.000272
Finnish	0.0000468	0.0000462
European (Non-Finnish)	0.000254	0.000237
Middle Eastern	0.000278	0.000272
South Asian	0.000327	0.000327
Other	0.000329	0.000326

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0862

Intolerance Scores

• loftool: 0.891
• rvis_EVS: 0.29
• rvis_percentile_EVS: 71.57

Haploinsufficiency Scores

• pHI: 0.0752
• hipred: N
• hipred_score: 0.198
• ghis: 0.479

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.147

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc41a3
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); renal/urinary system phenotype; homeostasis/metabolism phenotype

Gene ontology

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