SLC7A14
Basic information
Region (hg38): 3:170459548-170586075
Links
Phenotypes
GenCC
Source:
- retinitis pigmentosa (Supportive), mode of inheritance: AD
- retinitis pigmentosa 68 (Strong), mode of inheritance: AR
- retinitis pigmentosa 68 (Limited), mode of inheritance: Unknown
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Retinitis pigmentosa 68 | 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 | 24670872 |
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC7A14 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 | 133 | 144 | ||||
missense | 273 | 287 | ||||
nonsense | 7 | |||||
start loss | 0 | |||||
frameshift | 6 | |||||
inframe indel | 4 | |||||
splice donor/acceptor (+/-2bp) | 1 | |||||
splice region | 5 | 8 | 1 | 14 | ||
non coding | 26 | 31 | ||||
Total | 0 | 2 | 296 | 167 | 15 |
Variants in SLC7A14
This is a list of pathogenic ClinVar variants found in the SLC7A14 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
3-170467055-C-G | Uncertain significance (Aug 04, 2020) | |||
3-170467065-G-C | Uncertain significance (Sep 08, 2023) | |||
3-170467074-A-G | not specified | Uncertain significance (Dec 22, 2023) | ||
3-170467079-A-T | Uncertain significance (Feb 05, 2022) | |||
3-170467081-C-A | Retinal dystrophy | Uncertain significance (Oct 01, 2020) | ||
3-170467089-A-G | not specified • Retinal dystrophy | Uncertain significance (Oct 03, 2023) | ||
3-170467091-C-T | Likely benign (Aug 28, 2023) | |||
3-170467094-G-A | Benign (Dec 11, 2023) | |||
3-170467110-T-C | Uncertain significance (Oct 17, 2022) | |||
3-170467114-GTTTGCT-G | Uncertain significance (Jul 07, 2023) | |||
3-170467116-T-G | Uncertain significance (Dec 03, 2023) | |||
3-170467130-C-T | SLC7A14-related disorder | Likely benign (Jun 05, 2023) | ||
3-170467139-A-C | Uncertain significance (Oct 26, 2022) | |||
3-170467139-A-G | Likely benign (Feb 16, 2023) | |||
3-170467145-C-T | not specified | Benign/Likely benign (May 01, 2024) | ||
3-170467146-C-T | Retinal dystrophy | Uncertain significance (Oct 01, 2023) | ||
3-170467147-G-A | Uncertain significance (Apr 24, 2023) | |||
3-170467148-G-A | Likely benign (Jul 06, 2022) | |||
3-170467150-C-T | Uncertain significance (Dec 01, 2023) | |||
3-170467154-T-C | Likely benign (May 12, 2023) | |||
3-170467157-C-T | Likely benign (Nov 30, 2022) | |||
3-170467160-C-T | Likely benign (Jan 25, 2024) | |||
3-170467161-G-A | Benign (Jan 31, 2024) | |||
3-170467175-T-C | Likely benign (Aug 16, 2022) | |||
3-170467183-A-G | not specified | Uncertain significance (Jan 23, 2023) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
SLC7A14 | protein_coding | protein_coding | ENST00000231706 | 7 | 126492 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.0221 | 0.978 | 125725 | 0 | 22 | 125747 | 0.0000875 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.783 | 405 | 452 | 0.896 | 0.0000256 | 5001 |
Missense in Polyphen | 145 | 170.13 | 0.85228 | 1850 | ||
Synonymous | -0.0184 | 193 | 193 | 1.00 | 0.0000126 | 1607 |
Loss of Function | 3.35 | 8 | 26.7 | 0.300 | 0.00000134 | 317 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000210 | 0.000210 |
Ashkenazi Jewish | 0.0000992 | 0.0000992 |
East Asian | 0.000381 | 0.000381 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.0000706 | 0.0000703 |
Middle Eastern | 0.000381 | 0.000381 |
South Asian | 0.00 | 0.00 |
Other | 0.000168 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: May be involved in arginine transport. {ECO:0000269|PubMed:22787143, ECO:0000269|PubMed:24670872}.;
Recessive Scores
- pRec
- 0.123
Intolerance Scores
- loftool
- 0.0539
- rvis_EVS
- -1.08
- rvis_percentile_EVS
- 7.24
Haploinsufficiency Scores
- pHI
- 0.161
- hipred
- Y
- hipred_score
- 0.652
- ghis
- 0.551
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.343
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Slc7a14
- Phenotype
- vision/eye phenotype;
Zebrafish Information Network
- Gene name
- slc7a14a
- Affected structure
- trunk
- Phenotype tag
- abnormal
- Phenotype quality
- malformed
Gene ontology
- Biological process
- amino acid transport;negative regulation of phosphatase activity;transmembrane transport
- Cellular component
- lysosomal membrane;integral component of membrane
- Molecular function
- transmembrane transporter activity