14-68789856-G-C

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_004926.4(ZFP36L1):​c.694C>G​(p.Leu232Val) 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. 14/21 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

ZFP36L1
NM_004926.4 missense

Scores

2
17

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 3.23
Variant links:
Genes affected
ZFP36L1 (HGNC:1107): (ZFP36 ring finger protein like 1) This gene is a member of the TIS11 family of early response genes, which are induced by various agonists such as the phorbol ester TPA and the polypeptide mitogen EGF. This gene is well conserved across species and has a promoter that contains motifs seen in other early-response genes. The encoded protein contains a distinguishing putative zinc finger domain with a repeating cys-his motif. This putative nuclear transcription factor most likely functions in regulating the response to growth factors. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2011]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.13847625).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ZFP36L1NM_004926.4 linkc.694C>G p.Leu232Val missense_variant Exon 2 of 2 ENST00000439696.3 NP_004917.2 Q07352A0A024R658B3KNA8
ZFP36L1NM_001244701.1 linkc.901C>G p.Leu301Val missense_variant Exon 3 of 3 NP_001231630.1 Q07352
ZFP36L1NM_001244698.2 linkc.694C>G p.Leu232Val missense_variant Exon 2 of 3 NP_001231627.1 Q07352A0A024R658B3KNA8

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ZFP36L1ENST00000439696.3 linkc.694C>G p.Leu232Val missense_variant Exon 2 of 2 1 NM_004926.4 ENSP00000388402.2 Q07352
ZFP36L1ENST00000336440.4 linkc.694C>G p.Leu232Val missense_variant Exon 2 of 3 2 ENSP00000337386.3 Q07352
ZFP36L1ENST00000555997.1 linkn.898C>G non_coding_transcript_exon_variant Exon 2 of 2 3

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
31
GnomAD4 genome
Cov.:
32

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Aug 02, 2021
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.694C>G (p.L232V) alteration is located in exon 2 (coding exon 2) of the ZFP36L1 gene. This alteration results from a C to G substitution at nucleotide position 694, causing the leucine (L) at amino acid position 232 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.091
BayesDel_addAF
Benign
-0.26
T
BayesDel_noAF
Benign
-0.61
CADD
Benign
20
DANN
Benign
0.91
DEOGEN2
Benign
0.082
T;T
Eigen
Benign
-0.25
Eigen_PC
Benign
-0.17
FATHMM_MKL
Benign
0.72
D
LIST_S2
Uncertain
0.93
.;D
M_CAP
Benign
0.017
T
MetaRNN
Benign
0.14
T;T
MetaSVM
Benign
-1.1
T
MutationAssessor
Benign
1.7
L;L
PrimateAI
Uncertain
0.63
T
PROVEAN
Benign
-0.39
N;N
REVEL
Benign
0.072
Sift
Benign
0.080
T;T
Sift4G
Benign
0.50
T;T
Polyphen
0.85
P;P
Vest4
0.038
MutPred
0.42
Gain of catalytic residue at P228 (P = 0);Gain of catalytic residue at P228 (P = 0);
MVP
0.18
MPC
1.2
ClinPred
0.22
T
GERP RS
2.8
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1
Varity_R
0.071
gMVP
0.46

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.020
Details are displayed if max score is > 0.2

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr14-69256573; API