1-6593627-C-A

Variant names:

• chr1-6593627-C-A
• NM_014851.4:c.1532G>T

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2 PP3_Moderate

The NM_014851.4(KLHL21):​c.1532G>T​(p.Gly511Val) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 33)
• Consequence: KLHL21 NM_014851.4 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 7.57

Genes affected

KLHL21 (HGNC:29041): (kelch like family member 21) Enables cullin family protein binding activity. Contributes to ubiquitin-protein transferase activity. Involved in chromosome passenger complex localization to spindle midzone; protein ubiquitination; and regulation of cytokinesis. Located in polar microtubule. Part of Cul3-RING ubiquitin ligase complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Uncertain_significance. Variant got 4 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.886

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KLHL21	NM_014851.4	c.1532G>T	p.Gly511Val	missense_variant	Exon 4 of 4	ENST00000377658.8	NP_055666.2
KLHL21	NM_001324309.2	c.*481G>T		3_prime_UTR_variant	Exon 4 of 4		NP_001311238.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KLHL21	ENST00000377658.8	c.1532G>T	p.Gly511Val	missense_variant	Exon 4 of 4	1	NM_014851.4	ENSP00000366886.4
KLHL21	ENST00000496707.5	c.431G>T	p.Gly144Val	missense_variant	Exon 4 of 4	1		ENSP00000468710.1
KLHL21	ENST00000377663	c.*1738G>T		3_prime_UTR_variant	Exon 3 of 3	1		ENSP00000366891.3
KLHL21	ENST00000467612.5	c.431G>T	p.Gly144Val	missense_variant	Exon 4 of 4	3		ENSP00000466089.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 33

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Apr 04, 2023

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.1532G>T (p.G511V) alteration is located in exon 4 (coding exon 4) of the KLHL21 gene. This alteration results from a G to T substitution at nucleotide position 1532, causing the glycine (G) at amino acid position 511 to be replaced by a valine (V). 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	Pathogenic	0.80
BayesDel_addAF	Pathogenic	0.36	D
BayesDel_noAF	Pathogenic	0.29
CADD	Pathogenic	26
DANN	Uncertain	1.0
DEOGEN2	Benign	0.18	T;T;T
Eigen	Pathogenic	0.86
Eigen_PC	Pathogenic	0.79
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Uncertain	0.92	D;D;D
M_CAP	Uncertain	0.15	D
MetaRNN	Pathogenic	0.89	D;D;D
MetaSVM	Uncertain	0.34	D
MutationAssessor	Uncertain	2.4	M;.;.
PrimateAI	Pathogenic	0.83	D
PROVEAN	Pathogenic	-6.0	D;.;.
REVEL	Pathogenic	0.76
Sift	Uncertain	0.0020	D;.;.
Sift4G	Uncertain	0.0040	D;D;.
Polyphen		1.0	D;.;.
Vest4		0.88
MutPred		0.65		Gain of catalytic residue at G511 (P = 0.0057);.;.;
MVP		0.96
MPC		0.92
ClinPred		0.99	D
GERP RS		5.3
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.8
Varity_R		0.82
gMVP		0.68

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr1-6653687;