rs3798130

Variant names:

• chr5-132706454-C-A
• rs3798130
• NM_001300791.2:c.1306G>T

Your query was ambiguous. Multiple possible variants found:

• chr5-132706454-C-A
• chr5-132706454-C-G
• chr5-132706454-C-T

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001300791.2(KIF3A):​c.1306G>T​(p.Ala436Ser) 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. 13/18 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: KIF3A NM_001300791.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.96
• Publications: 25 publications found

Genes affected

KIF3A (HGNC:6319): (kinesin family member 3A) Enables protein phosphatase binding activity; small GTPase binding activity; and spectrin binding activity. Involved in protein localization to cell junction and protein transport. Located in centriole and centrosome. Part of kinesin II complex. Colocalizes with spindle microtubule. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000230612 (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.08395746).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001300791.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIF3A	NM_001300791.2	MANE Select	c.1306G>T	p.Ala436Ser	missense	Exon 11 of 19	NP_001287720.1	E9PES4
	KIF3A	NM_001300792.2		c.1234G>T	p.Ala412Ser	missense	Exon 10 of 18	NP_001287721.1	J3KPF9
	KIF3A	NM_007054.7		c.1229-2835G>T		intron	N/A	NP_008985.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIF3A	ENST00000403231.6	TSL:2 MANE Select	c.1306G>T	p.Ala436Ser	missense	Exon 11 of 19	ENSP00000385808.1	E9PES4
	KIF3A	ENST00000378735.5	TSL:1	c.1234G>T	p.Ala412Ser	missense	Exon 10 of 18	ENSP00000368009.1	J3KPF9
	KIF3A	ENST00000618515.4	TSL:5	c.1303G>T	p.Ala435Ser	missense	Exon 11 of 19	ENSP00000483023.1	A0A087X011

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 29

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.073
BayesDel_addAF	Benign	-0.093	T
BayesDel_noAF	Benign	-0.37
CADD	Uncertain	24
DANN	Benign	0.80
DEOGEN2	Benign	0.098	T
Eigen	Benign	-0.25
Eigen_PC	Benign	-0.087
FATHMM_MKL	Uncertain	0.87	D
LIST_S2	Benign	0.26	T
M_CAP	Benign	0.020	T
MetaRNN	Benign	0.084	T
MetaSVM	Benign	-0.88	T
PhyloP100		2.0
PROVEAN	Benign	0.060	N
REVEL	Benign	0.048
Sift	Benign	0.69	T
Sift4G	Benign	0.73	T
Polyphen		0.0060	B
Vest4		0.21
MutPred		0.17		Gain of phosphorylation at A436 (P = 0.0178)
MVP		0.50
ClinPred		0.21	T
GERP RS		3.6
gMVP		0.16
Mutation Taster		=93/7	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.090		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs3798130; hg19: chr5-132042146;