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GeneBe

16-85067283-G-C

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001388359.1(KIAA0513):c.212G>C(p.Arg71Pro) variant causes a missense change. The variant allele was found at a frequency of 0.00000434 in 1,613,782 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.000020 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000027 ( 0 hom. )

Consequence

KIAA0513
NM_001388359.1 missense

Scores

1
9
9

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 4.77
Variant links:
Genes affected
KIAA0513 (HGNC:29058): (KIAA0513) Predicted to be located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

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
KIAA0513NM_001388359.1 linkuse as main transcriptc.212G>C p.Arg71Pro missense_variant 2/13 ENST00000683363.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
KIAA0513ENST00000683363.1 linkuse as main transcriptc.212G>C p.Arg71Pro missense_variant 2/13 NM_001388359.1 A1O60268-1
KIAA0513ENST00000566428.5 linkuse as main transcriptc.212G>C p.Arg71Pro missense_variant 2/131 A1O60268-1
KIAA0513ENST00000567328.6 linkuse as main transcriptc.212G>C p.Arg71Pro missense_variant 2/81 O60268-2
KIAA0513ENST00000538274.6 linkuse as main transcriptc.212G>C p.Arg71Pro missense_variant 2/122 P4O60268-3

Frequencies

GnomAD3 genomes
AF:
0.0000197
AC:
3
AN:
152220
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000131
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.000478
GnomAD4 exome
AF:
0.00000274
AC:
4
AN:
1461562
Hom.:
0
Cov.:
31
AF XY:
0.00
AC XY:
0
AN XY:
727116
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.0000671
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.0000166
GnomAD4 genome
AF:
0.0000197
AC:
3
AN:
152220
Hom.:
0
Cov.:
32
AF XY:
0.0000134
AC XY:
1
AN XY:
74356
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.000131
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.000478
Bravo
AF:
0.0000113

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 submitterclinical testingAmbry GeneticsJan 04, 2024The c.212G>C (p.R71P) alteration is located in exon 2 (coding exon 1) of the KIAA0513 gene. This alteration results from a G to C substitution at nucleotide position 212, causing the arginine (R) at amino acid position 71 to be replaced by a proline (P). 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
0.26
BayesDel_addAF
Pathogenic
0.19
D
BayesDel_noAF
Uncertain
0.040
Cadd
Benign
21
Dann
Uncertain
1.0
DEOGEN2
Benign
0.063
T;.;T;.
Eigen
Uncertain
0.51
Eigen_PC
Uncertain
0.50
FATHMM_MKL
Uncertain
0.95
D
LIST_S2
Uncertain
0.90
D;D;.;D
M_CAP
Benign
0.022
T
MetaRNN
Uncertain
0.63
D;D;D;D
MetaSVM
Benign
-0.65
T
MutationAssessor
Uncertain
2.5
M;M;M;M
MutationTaster
Benign
1.0
D;D;D;D
PrimateAI
Benign
0.40
T
PROVEAN
Benign
-1.6
N;N;N;N
REVEL
Benign
0.17
Sift
Benign
0.034
D;D;D;D
Sift4G
Uncertain
0.055
T;T;T;D
Polyphen
0.90
P;.;P;.
Vest4
0.78
MutPred
0.23
Loss of stability (P = 0.0664);Loss of stability (P = 0.0664);Loss of stability (P = 0.0664);Loss of stability (P = 0.0664);
MVP
0.58
MPC
0.44
ClinPred
0.97
D
GERP RS
4.5
Varity_R
0.34
gMVP
0.49

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

LitVar

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

Other links and lift over

dbSNP: rs1177796146; hg19: chr16-85100889; API