LRRC75A
Basic information
Region (hg38): 17:16441576-16492193
Previous symbols: [ "C17orf76", "FAM211A" ]
Links
Phenotypes
GenCC
Source:
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 LRRC75A 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 | 4 | |||||
missense | 18 | 21 | ||||
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 | 6 | 1 |
Variants in LRRC75A
This is a list of pathogenic ClinVar variants found in the LRRC75A region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
17-16443644-C-T | not specified | Uncertain significance (Sep 29, 2023) | ||
17-16443686-C-T | not specified | Uncertain significance (May 24, 2023) | ||
17-16443766-C-T | not specified | Uncertain significance (Jan 23, 2023) | ||
17-16443866-T-C | not specified | Uncertain significance (Oct 13, 2023) | ||
17-16443894-G-T | not specified | Likely benign (Feb 13, 2024) | ||
17-16443901-C-T | not specified | Uncertain significance (May 02, 2024) | ||
17-16443931-C-T | Benign (Dec 20, 2017) | |||
17-16443936-C-T | not specified | Likely benign (Dec 16, 2023) | ||
17-16444060-C-T | not specified | Uncertain significance (Jul 13, 2021) | ||
17-16444065-G-A | not specified | Likely benign (May 24, 2023) | ||
17-16444100-C-T | not specified | Uncertain significance (Dec 14, 2022) | ||
17-16444102-G-T | not specified | Uncertain significance (Jun 07, 2023) | ||
17-16447876-G-A | not specified | Uncertain significance (Mar 29, 2022) | ||
17-16447923-C-T | not specified | Uncertain significance (Feb 26, 2024) | ||
17-16447942-C-T | not specified | Likely benign (Mar 27, 2023) | ||
17-16447957-C-T | not specified | Uncertain significance (Nov 17, 2023) | ||
17-16462272-G-A | not specified | Uncertain significance (Jan 26, 2023) | ||
17-16462303-G-A | Likely benign (Aug 01, 2022) | |||
17-16462328-C-T | not specified | Uncertain significance (May 26, 2023) | ||
17-16491839-T-C | not specified | Uncertain significance (Jan 16, 2024) | ||
17-16491849-T-G | not specified | Likely benign (Apr 07, 2023) | ||
17-16491878-C-G | not specified | Uncertain significance (Dec 15, 2023) | ||
17-16491923-C-T | not specified | Uncertain significance (Feb 07, 2023) | ||
17-16491939-C-T | not specified | Uncertain significance (Apr 09, 2024) | ||
17-16491955-C-G | not specified | Uncertain significance (May 29, 2024) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
LRRC75A | protein_coding | protein_coding | ENST00000470794 | 4 | 50577 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.696 | 0.301 | 125181 | 0 | 4 | 125185 | 0.0000160 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 1.11 | 141 | 183 | 0.769 | 0.0000120 | 2159 |
Missense in Polyphen | 79 | 108.48 | 0.72827 | 1131 | ||
Synonymous | -0.944 | 92 | 81.2 | 1.13 | 0.00000513 | 781 |
Loss of Function | 2.33 | 1 | 8.20 | 0.122 | 4.36e-7 | 103 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.0000906 | 0.0000906 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.00 | 0.00 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.0000184 | 0.0000177 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.00 | 0.00 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
Intolerance Scores
- loftool
- rvis_EVS
- 0.93
- rvis_percentile_EVS
- 89.66
Haploinsufficiency Scores
- pHI
- 0.228
- hipred
- N
- hipred_score
- 0.386
- ghis
Essentials
- essential_gene_CRISPR
- essential_gene_CRISPR2
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- gene_indispensability_score
Mouse Genome Informatics
- Gene name
- Lrrc75a
- Phenotype
Gene ontology
- Biological process
- Cellular component
- cytoplasm
- Molecular function