rs76319365

Variant summary

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

The NM_015634.4(KIFBP):​c.925G>A​(p.Glu309Lys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 32)

Consequence

KIFBP
NM_015634.4 missense

Scores

4
10
5

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 8.45
Variant links:
Genes affected
KIFBP (HGNC:23419): (kinesin family binding protein) This gene encodes a kinesin family member 1 binding protein that is characterized by two tetratrico peptide repeats. The encoded protein localizes to the mitochondria and may be involved in regulating transport of the mitochondria. Mutations in this gene are associated with Goldberg-Shprintzen megacolon syndrome. [provided by RefSeq, Mar 2010]

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 Protein UniProt
KIFBPNM_015634.4 linkuse as main transcriptc.925G>A p.Glu309Lys missense_variant 6/7 ENST00000361983.7 NP_056449.1
KIFBPXM_017016067.2 linkuse as main transcriptc.127G>A p.Glu43Lys missense_variant 3/4 XP_016871556.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
KIFBPENST00000361983.7 linkuse as main transcriptc.925G>A p.Glu309Lys missense_variant 6/71 NM_015634.4 ENSP00000354848 P1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
30
GnomAD4 genome
Cov.:
32

ClinVar

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

Submissions by phenotype

Goldberg-Shprintzen syndrome Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingGenetic Services Laboratory, University of ChicagoMar 04, 2013- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.85
BayesDel_addAF
Pathogenic
0.25
D
BayesDel_noAF
Uncertain
0.12
CADD
Pathogenic
28
DANN
Pathogenic
1.0
DEOGEN2
Benign
0.30
T;T
Eigen
Uncertain
0.60
Eigen_PC
Uncertain
0.66
FATHMM_MKL
Pathogenic
1.0
D
LIST_S2
Uncertain
0.93
D;D
M_CAP
Benign
0.019
T
MetaRNN
Uncertain
0.58
D;D
MetaSVM
Benign
-0.92
T
MutationAssessor
Uncertain
2.0
M;.
MutationTaster
Benign
1.0
D
PrimateAI
Uncertain
0.76
T
PROVEAN
Uncertain
-2.7
D;.
REVEL
Uncertain
0.34
Sift
Uncertain
0.016
D;.
Sift4G
Benign
0.096
T;.
Polyphen
0.96
D;.
Vest4
0.86
MutPred
0.45
Gain of MoRF binding (P = 0.0076);.;
MVP
0.68
MPC
1.2
ClinPred
0.95
D
GERP RS
5.4
Varity_R
0.52
gMVP
0.66

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: rs76319365; hg19: chr10-70770706; API