chr2-188483451-C-T
Position:
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_016315.4(GULP1):c.49C>T(p.Pro17Ser) variant causes a missense change. The variant allele was found at a frequency of 0.000000725 in 1,378,726 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 7.3e-7 ( 0 hom. )
Consequence
GULP1
NM_016315.4 missense
NM_016315.4 missense
Scores
2
10
6
Clinical Significance
Conservation
PhyloP100: 4.76
Genes affected
GULP1 (HGNC:18649): (GULP PTB domain containing engulfment adaptor 1) The protein encoded by this gene is an adapter protein necessary for the engulfment of apoptotic cells by phagocytes. Several transcript variants, some protein coding and some thought not to be protein coding, have been found for this gene. [provided by RefSeq, Nov 2011]
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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 | UniProt |
---|---|---|---|---|---|---|---|
GULP1 | NM_016315.4 | c.49C>T | p.Pro17Ser | missense_variant | 4/12 | ENST00000409830.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GULP1 | ENST00000409830.6 | c.49C>T | p.Pro17Ser | missense_variant | 4/12 | 1 | NM_016315.4 | P1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 genomes
Cov.:
33
GnomAD4 exome AF: 7.25e-7 AC: 1AN: 1378726Hom.: 0 Cov.: 21 AF XY: 0.00 AC XY: 0AN XY: 689240
GnomAD4 exome
AF:
AC:
1
AN:
1378726
Hom.:
Cov.:
21
AF XY:
AC XY:
0
AN XY:
689240
Gnomad4 AFR exome
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GnomAD4 genome Cov.: 33
GnomAD4 genome
Cov.:
33
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 08, 2023 | The c.49C>T (p.P17S) alteration is located in exon 4 (coding exon 2) of the GULP1 gene. This alteration results from a C to T substitution at nucleotide position 49, causing the proline (P) at amino acid position 17 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Uncertain
D
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;.;.;D;D;.;.;D;D
M_CAP
Benign
T
MetaRNN
Uncertain
T;T;T;T;T;T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;M;M;.;M;M;M;M;M
MutationTaster
Benign
D;D;D;D;D;D;D;N
PrimateAI
Uncertain
T
PROVEAN
Pathogenic
D;D;D;D;N;D;D;D;D
REVEL
Benign
Sift
Benign
D;D;D;D;D;D;D;D;D
Sift4G
Uncertain
D;D;T;T;T;D;D;T;D
Polyphen
0.0010, 0.98
.;B;D;.;.;B;B;D;B
Vest4
MutPred
Gain of MoRF binding (P = 0.0476);Gain of MoRF binding (P = 0.0476);Gain of MoRF binding (P = 0.0476);Gain of MoRF binding (P = 0.0476);Gain of MoRF binding (P = 0.0476);Gain of MoRF binding (P = 0.0476);Gain of MoRF binding (P = 0.0476);Gain of MoRF binding (P = 0.0476);Gain of MoRF binding (P = 0.0476);
MVP
MPC
0.18
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
Publications
No publications associated with this variant yet.