SLC9B1
Basic information
Region (hg38): 4:102885047-103019719
Previous symbols: [ "NHEDC1" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not provided (31 variants)
- Inborn genetic diseases (23 variants)
- Wolfram syndrome 2 (4 variants)
- not specified (2 variants)
- Usher syndrome (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC9B1 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 | 2 | |||||
missense | 20 | 26 | ||||
nonsense | 1 | |||||
start loss | 0 | |||||
frameshift | 1 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region ? | 1 | 1 | ||||
non coding ? | 15 | 24 | ||||
Total | 1 | 0 | 30 | 22 | 1 |
Variants in SLC9B1
This is a list of pathogenic ClinVar variants found in the SLC9B1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
4-102885206-A-G | Likely benign (Jul 25, 2022) | |||
4-102885207-C-A | Wolfram syndrome 2 • CISD2-related disorder | Benign/Likely benign (Dec 12, 2023) | ||
4-102885221-G-C | Wolfram syndrome 2 | Pathogenic (Oct 01, 2007) | ||
4-102885230-C-T | Uncertain significance (May 15, 2022) | |||
4-102885232-G-A | Likely benign (Jun 27, 2022) | |||
4-102885254-C-T | Uncertain significance (May 10, 2022) | |||
4-102885256-C-T | Likely benign (Jan 11, 2023) | |||
4-102885282-G-A | Uncertain significance (Aug 10, 2022) | |||
4-102885294-C-T | Uncertain significance (May 23, 2023) | |||
4-102885295-G-A | Likely benign (Aug 16, 2022) | |||
4-102885316-T-C | Likely benign (May 29, 2022) | |||
4-102885336-T-C | Uncertain significance (Jul 13, 2016) | |||
4-102885338-C-A | Uncertain significance (Feb 23, 2022) | |||
4-102885339-A-T | Uncertain significance (Jul 19, 2022) | |||
4-102885340-A-G | Likely benign (Mar 26, 2022) | |||
4-102885347-A-T | Uncertain significance (May 30, 2022) | |||
4-102885351-C-T | Wolfram syndrome 2 | Uncertain significance (Aug 01, 2022) | ||
4-102885352-G-A | Wolfram syndrome 2 | Benign/Likely benign (Nov 20, 2023) | ||
4-102885376-T-A | Likely benign (Jun 16, 2022) | |||
4-102885406-T-C | Likely benign (Jan 19, 2024) | |||
4-102885410-A-G | Uncertain significance (Jul 12, 2021) | |||
4-102885412-G-A | Likely benign (Aug 31, 2022) | |||
4-102885446-A-T | Likely benign (Oct 24, 2022) | |||
4-102885447-C-T | Likely benign (Apr 12, 2023) | |||
4-102885448-G-A | Likely benign (May 23, 2023) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
SLC9B1 | protein_coding | protein_coding | ENST00000296422 | 11 | 134692 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
5.17e-7 | 0.864 | 125513 | 0 | 217 | 125730 | 0.000863 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.874 | 218 | 257 | 0.847 | 0.0000122 | 3271 |
Missense in Polyphen | 44 | 65.753 | 0.66917 | 849 | ||
Synonymous | 1.14 | 77 | 90.9 | 0.847 | 0.00000442 | 1022 |
Loss of Function | 1.54 | 13 | 20.6 | 0.632 | 8.67e-7 | 287 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000755 | 0.000737 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.00 | 0.00 |
Finnish | 0.000235 | 0.000231 |
European (Non-Finnish) | 0.00108 | 0.00103 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.00242 | 0.00235 |
Other | 0.000170 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Sperm-specific Na(+)/H(+) exchanger involved in intracellular pH regulation of spermatozoa. Involved in sperm motility and fertility. {ECO:0000250|UniProtKB:Q8C0X2}.;
- Pathway
- Stimuli-sensing channels;Ion channel transport;Transport of small molecules
(Consensus)
Recessive Scores
- pRec
- 0.0840
Intolerance Scores
- loftool
- rvis_EVS
- 0.26
- rvis_percentile_EVS
- 70.44
Haploinsufficiency Scores
- pHI
- 0.172
- hipred
- N
- hipred_score
- 0.218
- ghis
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.114
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Slc9b1
- Phenotype
Gene ontology
- Biological process
- single fertilization;flagellated sperm motility;ion transmembrane transport;sodium ion transmembrane transport;regulation of intracellular pH;proton transmembrane transport
- Cellular component
- plasma membrane;integral component of membrane;sperm principal piece
- Molecular function
- sodium:proton antiporter activity