SLC25A39

solute carrier family 25 member 39, the group of Solute carrier family 25

Basic information

Region (hg38): 17:44319625-44324870

Links

ENSG00000013306 ∙ NCBI:51629 ∙ OMIM:610820 ∙ HGNC:24279 ∙ Uniprot:Q9BZJ4 ∙ 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 SLC25A39 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC25A39 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			45	2		47
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	45	3	0

Variants in SLC25A39

This is a list of pathogenic ClinVar variants found in the SLC25A39 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-44320006-C-T		not specified	Likely benign (Jul 05, 2022)
17-44320019-G-C		not specified	Likely benign (Dec 31, 2024)
17-44320041-A-C		not specified	Uncertain significance (Nov 03, 2023)
17-44320051-C-T		not specified	Uncertain significance (Aug 13, 2021)
17-44320083-G-A		not specified	Uncertain significance (Sep 11, 2024)
17-44320105-G-A		not specified	Uncertain significance (Oct 01, 2024)
17-44320219-G-A		not specified	Uncertain significance (Dec 28, 2022)
17-44320228-C-T		not specified	Uncertain significance (Feb 13, 2024)
17-44320361-C-T		not specified	Uncertain significance (May 07, 2024)
17-44320372-G-A		not specified	Uncertain significance (Dec 17, 2023)
17-44320391-G-A		not specified	Uncertain significance (Jul 31, 2024)
17-44320623-G-A		not specified	Likely benign (Jan 18, 2023)
17-44320642-C-T		not specified	Uncertain significance (Jul 14, 2021)
17-44320713-T-C		not specified	Uncertain significance (Nov 06, 2023)
17-44320716-T-G		not specified	Uncertain significance (Aug 28, 2024)
17-44320722-C-A		not specified	Uncertain significance (Aug 27, 2024)
17-44320728-A-G		not specified	Uncertain significance (Feb 26, 2025)
17-44321112-G-A		not specified	Uncertain significance (May 03, 2023)
17-44321165-G-A		not specified • EBV-positive nodal T- and NK-cell lymphoma	Uncertain significance (Jan 16, 2024)
17-44321168-A-C		not specified	Uncertain significance (Mar 16, 2023)
17-44321171-T-C		not specified	Uncertain significance (Oct 19, 2024)
17-44321193-G-A		not specified	Uncertain significance (Nov 10, 2022)
17-44321194-C-G		not specified	Uncertain significance (Feb 10, 2025)
17-44321194-C-T		not specified	Uncertain significance (Dec 10, 2024)
17-44321437-G-A		not specified	Uncertain significance (Aug 10, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC25A39	protein_coding	protein_coding	ENST00000377095	11	5246

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.40e-11	0.213	125693	0	52	125745	0.000207

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.296	212	224	0.944	0.0000141	2267
Missense in Polyphen		54	64.069	0.84285		655
Synonymous	-3.14	129	90.9	1.42	0.00000555	782
Loss of Function	0.762	18	21.8	0.824	0.00000122	211

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000681	0.000677
Ashkenazi Jewish	0.0000994	0.0000992
East Asian	0.000386	0.000381
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000134	0.000132
Middle Eastern	0.000386	0.000381
South Asian	0.000261	0.000261
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for normal heme biosynthesis. {ECO:0000250}.

Recessive Scores

• pRec: 0.107

Intolerance Scores

• loftool: 0.744
• rvis_EVS: -1
• rvis_percentile_EVS: 8.37

Haploinsufficiency Scores

• pHI: 0.136
• hipred: N
• hipred_score: 0.289
• ghis: 0.550

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0638

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc25a39

Zebrafish Information Network

• Gene name: slc25a39
• Affected structure: nucleate erythrocyte
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: heme biosynthetic process;transmembrane transport
• Cellular component: mitochondrial inner membrane;integral component of membrane
• Molecular function: transmembrane transporter activity