GeneBe

rs753531974

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 4P and 4B. PM1PM2BP4_Strong

The NM_001443.3(FABP1):​c.166T>A​(p.Ser56Thr) 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. 16/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 32)

Consequence

FABP1
NM_001443.3 missense

Scores

18

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: -0.590

Publications

0 publications found
Variant links:
Genes affected
FABP1 (HGNC:3555): (fatty acid binding protein 1) This gene encodes the fatty acid binding protein found in liver. Fatty acid binding proteins are a family of small, highly conserved, cytoplasmic proteins that bind long-chain fatty acids and other hydrophobic ligands. This protein and FABP6 (the ileal fatty acid binding protein) are also able to bind bile acids. It is thought that FABPs roles include fatty acid uptake, transport, and metabolism. [provided by RefSeq, Mar 2011]

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

PM1
In a modified_residue Phosphoserine (size 0) in uniprot entity FABPL_HUMAN
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.04870683).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001443.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
FABP1
NM_001443.3
MANE Select
c.166T>Ap.Ser56Thr
missense
Exon 2 of 4NP_001434.1P07148

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
FABP1
ENST00000295834.8
TSL:1 MANE Select
c.166T>Ap.Ser56Thr
missense
Exon 2 of 4ENSP00000295834.3P07148
FABP1
ENST00000877228.1
c.166T>Ap.Ser56Thr
missense
Exon 2 of 5ENSP00000547287.1
FABP1
ENST00000393750.3
TSL:2
c.166T>Ap.Ser56Thr
missense
Exon 2 of 3ENSP00000377351.3A8MW49

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD2 exomes
AF:
0.00000398
AC:
1
AN:
251466
AF XY:
0.00000736
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00000879
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
Cov.:
30
GnomAD4 genome
Cov.:
32

ClinVar

ClinVar submissions
Significance:Uncertain significance
Revision:criteria provided, single submitter
View on ClinVar
Pathogenic
VUS
Benign
Condition
-
1
-
not specified (1)

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.073
BayesDel_addAF
Benign
-0.31
T
BayesDel_noAF
Benign
-0.68
CADD
Benign
0.30
DANN
Benign
0.46
DEOGEN2
Benign
0.028
T
Eigen
Benign
-1.4
Eigen_PC
Benign
-1.5
FATHMM_MKL
Benign
0.10
N
LIST_S2
Benign
0.61
T
M_CAP
Benign
0.0081
T
MetaRNN
Benign
0.049
T
MetaSVM
Benign
-0.97
T
MutationAssessor
Benign
1.1
L
PhyloP100
-0.59
PrimateAI
Benign
0.32
T
PROVEAN
Benign
-1.3
N
REVEL
Benign
0.024
Sift
Benign
0.36
T
Sift4G
Benign
0.77
T
Polyphen
0.0
B
Vest4
0.16
MutPred
0.37
Gain of phosphorylation at S56 (P = 0.0805)
MVP
0.099
MPC
0.23
ClinPred
0.17
T
GERP RS
-8.7
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1
Varity_R
0.27
gMVP
0.42
Mutation Taster
=95/5
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: rs753531974; hg19: chr2-88425769; API