SLC25A28

solute carrier family 25 member 28, the group of Solute carrier family 25

Basic information

Region (hg38): 10:99610518-99622793

Links

ENSG00000155287 ∙ NCBI:81894 ∙ OMIM:609767 ∙ HGNC:23472 ∙ Uniprot:Q96A46 ∙ 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 SLC25A28 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC25A28 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						0
missense			18			18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	0	0

Variants in SLC25A28

This is a list of pathogenic ClinVar variants found in the SLC25A28 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-99610919-G-A		not specified	Uncertain significance (Dec 18, 2023)
10-99610938-T-C		not specified	Uncertain significance (May 31, 2023)
10-99610980-T-C		not specified	Uncertain significance (Mar 01, 2024)
10-99610992-C-T		not specified	Uncertain significance (May 18, 2022)
10-99611124-C-T		not specified	Uncertain significance (Apr 08, 2022)
10-99613845-G-A		not specified	Uncertain significance (Jun 04, 2024)
10-99620158-C-T		not specified	Uncertain significance (Apr 08, 2022)
10-99620185-G-C		not specified	Uncertain significance (Sep 20, 2023)
10-99620202-T-A		not specified	Uncertain significance (Jul 06, 2021)
10-99620202-T-C		not specified	Uncertain significance (Oct 06, 2021)
10-99620202-T-G		not specified	Uncertain significance (Aug 13, 2021)
10-99620214-G-C		not specified	Uncertain significance (Oct 05, 2023)
10-99620215-C-T		not specified	Uncertain significance (Oct 05, 2023)
10-99620220-C-A		not specified	Uncertain significance (Nov 02, 2023)
10-99620226-A-C		not specified	Uncertain significance (Nov 19, 2021)
10-99620256-G-A		not specified	Uncertain significance (Dec 21, 2022)
10-99620293-G-A		not specified	Uncertain significance (Oct 03, 2023)
10-99620301-G-A		not specified	Uncertain significance (Feb 05, 2024)
10-99620304-A-C		not specified	Uncertain significance (Aug 16, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC25A28	protein_coding	protein_coding	ENST00000370495	4	10085

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.930	0.0704	124790	0	4	124794	0.0000160

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.92	82	197	0.416	0.0000111	2335
Missense in Polyphen		15	82.328	0.1822		915
Synonymous	0.560	74	80.4	0.921	0.00000497	771
Loss of Function	3.06	1	12.9	0.0778	6.42e-7	144

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000684	0.0000556
Finnish	0.00	0.00
European (Non-Finnish)	0.0000265	0.0000265
Middle Eastern	0.0000684	0.0000556
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Mitochondrial iron transporter that mediates iron uptake. Probably required for heme synthesis of hemoproteins and Fe-S cluster assembly in non-erythroid cells. The iron delivered into the mitochondria, presumably as Fe(2+), is then probably delivered to ferrochelatase to catalyze Fe(2+) incorporation into protoprophyrin IX to make heme (By similarity). {ECO:0000250}.
• Pathway: Mitochondrial iron-sulfur cluster biogenesis;Metabolism (Consensus)

Recessive Scores

• pRec: 0.149

Intolerance Scores

• loftool: 0.166
• rvis_EVS: -0.38
• rvis_percentile_EVS: 27.42

Haploinsufficiency Scores

• pHI: 0.420
• hipred: Y
• hipred_score: 0.728
• ghis: 0.534

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.505

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc25a28
• Phenotype: immune system phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: iron import into the mitochondrion;iron ion homeostasis
• Cellular component: mitochondrial inner membrane;integral component of membrane
• Molecular function: iron ion transmembrane transporter activity