NM_001364564.1:c.2267C>A

Variant summary

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

The NM_001364564.1(SALL2):​c.2267C>A​(p.Pro756Gln) 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. 13/19 in silico tools predict 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. P756R) has been classified as Benign.

Frequency

Genomes: not found (cov: 32)

Consequence

SALL2
NM_001364564.1 missense

Scores

1
17

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.19
Variant links:
Genes affected
SALL2 (HGNC:10526): (spalt like transcription factor 2) This gene encodes a protein containing multiple zinc finger domains. The encoded protein functions in optical fissure closure during development of the eye in the embryo. Mutations in this gene are associated with ocular coloboma. [provided by RefSeq, Jul 2016]

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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=0.10224402).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SALL2NM_001364564.1 linkc.2267C>A p.Pro756Gln missense_variant Exon 2 of 2 ENST00000537235.2 NP_001351493.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SALL2ENST00000537235.2 linkc.2267C>A p.Pro756Gln missense_variant Exon 2 of 2 2 NM_001364564.1 ENSP00000438493.2 F5H433

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
34
GnomAD4 genome
Cov.:
32
TwinsUK
AF:
0.00
AC:
0
ALSPAC
AF:
0.000259
AC:
1

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.11
BayesDel_addAF
Benign
-0.24
T
BayesDel_noAF
Benign
-0.59
CADD
Benign
5.3
DANN
Uncertain
0.98
DEOGEN2
Benign
0.028
.;T
Eigen
Benign
-0.70
Eigen_PC
Benign
-0.71
FATHMM_MKL
Benign
0.25
N
LIST_S2
Benign
0.60
.;T
M_CAP
Benign
0.012
T
MetaRNN
Benign
0.10
T;T
MetaSVM
Benign
-0.99
T
PrimateAI
Benign
0.36
T
PROVEAN
Benign
-1.8
.;N
REVEL
Benign
0.045
Sift
Benign
0.16
.;T
Sift4G
Benign
0.36
T;T
Polyphen
0.80
.;P
Vest4
0.23
MutPred
0.21
Loss of glycosylation at P758 (P = 0.032);.;
MVP
0.32
ClinPred
0.27
T
GERP RS
3.0
gMVP
0.29

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs372214185; hg19: chr14-21991589; API