rs3743601
Positions:
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001077418.3(TMEM231):c.16C>T(p.Leu6Phe) variant causes a missense change. The variant allele was found at a frequency of 0.0000015 in 1,332,992 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 0.0000015 ( 0 hom. )
Consequence
TMEM231
NM_001077418.3 missense
NM_001077418.3 missense
Scores
1
8
8
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 3.96
Genes affected
TMEM231 (HGNC:37234): (transmembrane protein 231) This gene encodes a transmembrane protein, which is a component of the B9 complex involved in the formation of the diffusion barrier between the cilia and plasma membrane. Mutations in this gene cause Joubert syndrome (JBTS). Multiple alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jan 2013]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TMEM231 | NM_001077418.3 | c.16C>T | p.Leu6Phe | missense_variant | 1/7 | ENST00000258173.11 | NP_001070886.1 | |
TMEM231 | NM_001077416.2 | c.78C>T | p.Ser26= | synonymous_variant | 1/6 | NP_001070884.2 | ||
TMEM231 | NR_074083.2 | n.59C>T | non_coding_transcript_exon_variant | 1/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TMEM231 | ENST00000258173.11 | c.16C>T | p.Leu6Phe | missense_variant | 1/7 | 1 | NM_001077418.3 | ENSP00000258173 | P1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 genomes
Cov.:
33
GnomAD4 exome AF: 0.00000150 AC: 2AN: 1332992Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 651880
GnomAD4 exome
AF:
AC:
2
AN:
1332992
Hom.:
Cov.:
31
AF XY:
AC XY:
0
AN XY:
651880
Gnomad4 AFR exome
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GnomAD4 genome Cov.: 33
GnomAD4 genome
Cov.:
33
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Uncertain
CADD
Benign
DANN
Uncertain
DEOGEN2
Benign
T;T
Eigen
Benign
Eigen_PC
Uncertain
FATHMM_MKL
Benign
N
LIST_S2
Uncertain
D;D
M_CAP
Uncertain
D
MetaRNN
Uncertain
D;D
MetaSVM
Benign
T
MutationTaster
Benign
P;P;P
PROVEAN
Benign
N;N
REVEL
Uncertain
Sift
Benign
T;T
Sift4G
Uncertain
D;D
Polyphen
P;.
Vest4
MutPred
Loss of stability (P = 0.0341);Loss of stability (P = 0.0341);
MVP
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at