SLC38A8

solute carrier family 38 member 8, the group of Solute carrier family 38

Basic information

Region (hg38): 16:84009666-84042795

Links

ENSG00000166558 ∙ NCBI:146167 ∙ OMIM:615585 ∙ HGNC:32434 ∙ Uniprot:A6NNN8 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• foveal hypoplasia - optic nerve decussation defect - anterior segment dysgenesis syndrome (Strong), mode of inheritance: AR
• foveal hypoplasia - optic nerve decussation defect - anterior segment dysgenesis syndrome (Supportive), mode of inheritance: AR
• foveal hypoplasia - optic nerve decussation defect - anterior segment dysgenesis syndrome (Definitive), mode of inheritance: AR
• foveal hypoplasia - optic nerve decussation defect - anterior segment dysgenesis syndrome (Definitive), mode of inheritance: AR
• foveal hypoplasia - optic nerve decussation defect - anterior segment dysgenesis syndrome (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Foveal hypoplasia 2	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Ophthalmologic	24045842; 24290379

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC38A8 gene.

• not provided (203 variants)
• Inborn genetic diseases (37 variants)
• Foveal hypoplasia - optic nerve decussation defect - anterior segment dysgenesis syndrome (17 variants)
• not specified (5 variants)
• Foveal hypoplasia (2 variants)
• Foveal hypoplasia 2 and optic nerve misrouting with or without anterior segment dysgenesis (1 variants)
• Leber congenital amaurosis (1 variants)
• FOVEAL HYPOPLASIA 2 WITH OPTIC NERVE MISROUTING AND ANTERIOR SEGMENT DYSGENESIS (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC38A8 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				58	14	72
missense	2	1	53	11	8	75
nonsense	5	2				7
start loss						0
frameshift	6	1				7
inframe indel						0
splice donor/acceptor (+/-2bp)	1	4	1			6
splice region			2	16	3	21
non coding			1	22	28	51
Total	14	8	55	91	50

Highest pathogenic variant AF is 0.0000329

Variants in SLC38A8

This is a list of pathogenic ClinVar variants found in the SLC38A8 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-84009775-A-G			Benign (Oct 08, 2018)
16-84009787-G-C		SLC38A8-related disorder	Benign/Likely benign (Jan 31, 2024)
16-84009799-G-A			Likely benign (Dec 20, 2023)
16-84009799-G-T			Likely benign (Jan 11, 2024)
16-84009801-C-T		SLC38A8-related disorder	Likely benign (Jan 30, 2024)
16-84009802-C-A			Benign (Jan 28, 2024)
16-84009802-C-T			Likely benign (Jan 28, 2024)
16-84009803-G-A		Inborn genetic diseases	Uncertain significance (Nov 01, 2022)
16-84009808-C-G			Likely benign (Jan 12, 2024)
16-84009808-C-T			Likely benign (Dec 20, 2023)
16-84009811-C-T			Likely benign (Nov 18, 2022)
16-84009812-G-A			Benign (Jan 31, 2024)
16-84009814-G-A			Likely benign (Jun 04, 2023)
16-84009815-C-G		Inborn genetic diseases	Uncertain significance (Jun 06, 2023)
16-84009816-T-C		Inborn genetic diseases	Uncertain significance (May 25, 2022)
16-84009832-G-C			Likely benign (Feb 10, 2023)
16-84009836-C-A			Uncertain significance (Jan 10, 2020)
16-84009838-G-A			Likely benign (Jan 03, 2024)
16-84009841-C-T			Likely benign (Oct 08, 2023)
16-84009843-G-A			Likely benign (Jan 31, 2024)
16-84009844-C-T			Likely benign (Feb 28, 2023)
16-84009849-A-C			Uncertain significance (Aug 31, 2021)
16-84009850-G-C			Likely benign (Jan 31, 2024)
16-84009858-C-T		FOVEAL HYPOPLASIA 2 WITH OPTIC NERVE MISROUTING	Pathogenic (Dec 05, 2013)
16-84009870-G-A			Likely benign (Oct 25, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC38A8	protein_coding	protein_coding	ENST00000299709	10	32970

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.32e-24	0.0000100	125653	0	95	125748	0.000378

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-4.34	472	271	1.74	0.0000163	2761
Missense in Polyphen		175	104.68	1.6718		1153
Synonymous	-7.31	225	122	1.84	0.00000834	939
Loss of Function	-2.06	30	20.1	1.50	9.54e-7	215

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00119	0.00118
Ashkenazi Jewish	0.00	0.00
East Asian	0.000709	0.000707
Finnish	0.0000925	0.0000924
European (Non-Finnish)	0.000267	0.000264
Middle Eastern	0.000709	0.000707
South Asian	0.000720	0.000719
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Putative sodium-dependent amino acid/proton antiporter. {ECO:0000250}.

Intolerance Scores

• loftool: 0.885
• rvis_EVS: -0.94
• rvis_percentile_EVS: 9.41

Haploinsufficiency Scores

• pHI: 0.114
• ghis: 0.406

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.239

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc38a8

Gene ontology

• Biological process: amino acid transmembrane transport;sodium ion transport
• Cellular component: integral component of membrane
• Molecular function: amino acid transmembrane transporter activity