GeneBe

rs2037611709

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 1 ACMG points: 2P and 1B. PM2BP4

The NM_015656.2(KIF26A):​c.94C>G​(p.Pro32Ala) 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. 13/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 34)

Consequence

KIF26A
NM_015656.2 missense

Scores

2
2
13

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.850

Publications

0 publications found
Variant links:
Genes affected
KIF26A (HGNC:20226): (kinesin family member 26A) Predicted to enable microtubule binding activity and microtubule motor activity. Predicted to be involved in enteric nervous system development; negative regulation of signal transduction; and regulation of cell growth by extracellular stimulus. Predicted to be located in cytosol. Predicted to be part of kinesin complex. Predicted to be active in microtubule. [provided by Alliance of Genome Resources, Apr 2022]
KIF26A Gene-Disease associations (from GenCC):
  • complex cortical dysplasia with other brain malformations
    Inheritance: AR Classification: STRONG Submitted by: ClinGen
  • cortical dysplasia, complex, with other brain malformations 11
    Inheritance: AR Classification: STRONG, MODERATE, LIMITED Submitted by: Ambry Genetics, Baylor College of Medicine Research Center, Labcorp Genetics (formerly Invitae)

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.33719224).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015656.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
KIF26A
NM_015656.2
MANE Select
c.94C>Gp.Pro32Ala
missense
Exon 2 of 15NP_056471.1Q9ULI4

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
KIF26A
ENST00000423312.7
TSL:5 MANE Select
c.94C>Gp.Pro32Ala
missense
Exon 2 of 15ENSP00000388241.2Q9ULI4
KIF26A
ENST00000315264.7
TSL:1
c.-324C>G
5_prime_UTR
Exon 1 of 14ENSP00000325452.7C9JFF0
KIF26A
ENST00000697132.1
c.190C>Gp.Pro64Ala
missense
Exon 2 of 15ENSP00000513129.1A0A8V8TM02

Frequencies

GnomAD3 genomes
Cov.:
34
GnomAD4 exome
Cov.:
31
GnomAD4 genome
Cov.:
34
Alfa
AF:
0.00
Hom.:
0

ClinVar

ClinVar submissions
Significance:Uncertain significance
Revision:criteria provided, single submitter
View on ClinVar
Pathogenic
VUS
Benign
Condition
-
1
-
not specified (1)

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.064
BayesDel_addAF
Benign
-0.069
T
BayesDel_noAF
Benign
-0.34
CADD
Benign
17
DANN
Uncertain
0.99
Eigen
Benign
-0.41
Eigen_PC
Benign
-0.47
FATHMM_MKL
Benign
0.088
N
LIST_S2
Benign
0.50
T
M_CAP
Pathogenic
0.98
D
MetaRNN
Benign
0.34
T
MetaSVM
Benign
-0.71
T
MutationAssessor
Benign
0.90
L
PhyloP100
0.85
PrimateAI
Pathogenic
0.90
D
PROVEAN
Uncertain
-2.4
N
REVEL
Benign
0.21
Sift
Benign
0.20
T
Sift4G
Benign
0.21
T
Polyphen
0.84
P
Vest4
0.14
MutPred
0.26
Gain of relative solvent accessibility (P = 0.0082)
MVP
0.85
MPC
3.4
ClinPred
0.50
D
GERP RS
1.9
PromoterAI
0.017
Neutral
Varity_R
0.060
gMVP
0.24
Mutation Taster
=87/13
polymorphism

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

Other links and lift over

dbSNP: rs2037611709; hg19: chr14-104605431; API