GeneBe

rs1249355657

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 1 ACMG points: 2P and 1B. PM2BP4

The NM_001080533.3(UNC119B):​c.173C>A​(p.Thr58Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T58M) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

UNC119B
NM_001080533.3 missense

Scores

2
5
11

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.55

Publications

0 publications found
Variant links:
Genes affected
UNC119B (HGNC:16488): (unc-119 lipid binding chaperone B) Enables lipid binding activity. Involved in cilium assembly and lipoprotein transport. Located in ciliary transition zone. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.3173805).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001080533.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
UNC119B
NM_001080533.3
MANE Select
c.173C>Ap.Thr58Lys
missense
Exon 1 of 5NP_001074002.1A6NIH7

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
UNC119B
ENST00000344651.5
TSL:2 MANE Select
c.173C>Ap.Thr58Lys
missense
Exon 1 of 5ENSP00000344942.4A6NIH7
UNC119B
ENST00000718082.1
c.173C>Ap.Thr58Lys
missense
Exon 1 of 4ENSP00000520660.1A0ABB0MV57
UNC119B
ENST00000953441.1
c.173C>Ap.Thr58Lys
missense
Exon 1 of 3ENSP00000623500.1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
1296448
Hom.:
0
Cov.:
33
AF XY:
0.00
AC XY:
0
AN XY:
639168
African (AFR)
AF:
0.00
AC:
0
AN:
26234
American (AMR)
AF:
0.00
AC:
0
AN:
23294
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
22582
East Asian (EAS)
AF:
0.00
AC:
0
AN:
27604
South Asian (SAS)
AF:
0.00
AC:
0
AN:
70294
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
32182
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
3802
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
1037038
Other (OTH)
AF:
0.00
AC:
0
AN:
53418
GnomAD4 genome
Cov.:
32
Alfa
AF:
0.00
Hom.:
0
Bravo
AF:
0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
0.48
BayesDel_addAF
Benign
-0.019
T
BayesDel_noAF
Benign
-0.26
CADD
Uncertain
25
DANN
Uncertain
0.98
DEOGEN2
Benign
0.23
T
Eigen
Benign
0.11
Eigen_PC
Benign
0.10
FATHMM_MKL
Benign
0.63
D
LIST_S2
Benign
0.66
T
M_CAP
Pathogenic
0.62
D
MetaRNN
Benign
0.32
T
MetaSVM
Benign
-0.89
T
MutationAssessor
Uncertain
2.2
M
PhyloP100
3.6
PrimateAI
Pathogenic
0.92
D
PROVEAN
Uncertain
-3.0
D
REVEL
Benign
0.28
Sift
Uncertain
0.015
D
Sift4G
Benign
0.16
T
Polyphen
0.67
P
Vest4
0.35
MutPred
0.40
Gain of ubiquitination at T58 (P = 0.0094)
MVP
0.043
MPC
0.87
ClinPred
0.98
D
GERP RS
1.4
PromoterAI
-0.0091
Neutral
Varity_R
0.23
gMVP
0.72
Mutation Taster
=78/22
polymorphism

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs1249355657; hg19: chr12-121148450; API