rs28937877

Positions:

• chr16-75479308-T-C

Variant summary

Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PM2 PP3_Strong PP5_Moderate

The NM_021615.5(CHST6):​c.521A>G​(p.Lys174Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000411 in 1,460,970 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★). Synonymous variant affecting the same amino acid position (i.e. K174K) has been classified as Likely benign.

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 0.0000041 (0 hom.)
• Consequence: CHST6 NM_021615.5 missense
• Clinical Significance: Pathogenic criteria provided, single submitter P:2
• Conservation: PhyloP100: 7.91

Genes affected

CHST6 (HGNC:6938): (carbohydrate sulfotransferase 6) The protein encoded by this gene is an enzyme that catalyzes the transfer of a sulfate group to the GlcNAc residues of keratan. Keratan sulfate helps maintain corneal transparency. Defects in this gene are a cause of macular corneal dystrophy (MCD). [provided by RefSeq, Jan 2010]

(HGNC:):

ACMG classification

Verdict is Likely_pathogenic. Variant got 8 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.989
• PP5: Variant 16-75479308-T-C is Pathogenic according to our data. Variant chr16-75479308-T-C is described in ClinVar as [Pathogenic]. Clinvar id is 5071.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-75479308-T-C is described in UniProt as null. Variant chr16-75479308-T-C is described in UniProt as null. Variant chr16-75479308-T-C is described in UniProt as null. Variant chr16-75479308-T-C is described in UniProt as null. Variant chr16-75479308-T-C is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CHST6	NM_021615.5	c.521A>G	p.Lys174Arg	missense_variant	3/3	ENST00000332272.9
CHST6	NR_163480.1	n.733+2509A>G		intron_variant, non_coding_transcript_variant
CHST6	NR_163481.1	n.577+2509A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CHST6	ENST00000332272.9	c.521A>G	p.Lys174Arg	missense_variant	3/3	3	NM_021615.5	P1
	ENST00000530512.3	n.425+2988T>C		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 0.00000411 AC: 6 AN: 1460970 Hom.: 0 Cov.: 31 AF XY: 0.00000413 AC XY: 3 AN XY: 726840

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.000151

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 33

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:2

Revision: criteria provided, single submitter

Submissions by phenotype

Macular corneal dystrophy Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Apr 27, 2017	The CHST6 c.521A>G (p.Lys174Arg) missense variant has been reported in two studies in which it is found in a total of four patients with macular corneal dystrophy, including in three in a homozygous state and in one in a compound heterozygous state with a second missense variant (Akama et al. 2000; Park et al. 2015). The p.Lys174Arg variant was absent from 162 control chromosomes and was not found in the 1000 Genomes Project, the Exome Sequencing Project, or the Exome Aggregation Consortium in a region of good coverage, so is presumed to be rare. The Lys174 residue is highly conserved amongst sulfotransferases. Functional studies in HeLa cells demonstrated that the p.Lys174Arg variant resulted in a loss of enzyme activity and a failure of the CHST6 protein to produce highly sulphated keratin sulfate, which would result in the accumulation of non-sulfated keratin sulfate within the keratocytes and corneal epithelium, which is characteristic of macular corneal dystrophy (Akama et al. 2001). Based on the evidence, the p.Lys174Arg variant is classified as pathogenic for macular corneal dystrophy. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population. -
Pathogenic, no assertion criteria provided	literature only	OMIM	Oct 01, 2000	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.69
BayesDel_addAF	Pathogenic	0.54	D
BayesDel_noAF	Pathogenic	0.54
CADD	Pathogenic	28
DANN	Uncertain	1.0
DEOGEN2	Pathogenic	0.94	D;D;D
Eigen	Pathogenic	0.80
Eigen_PC	Pathogenic	0.71
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Pathogenic	0.98	.;.;D
M_CAP	Pathogenic	0.94	D
MetaRNN	Pathogenic	0.99	D;D;D
MetaSVM	Pathogenic	1.0	D
MutationAssessor	Pathogenic	3.4	M;M;M
MutationTaster	Benign	1.0	A;A
PrimateAI	Uncertain	0.74	T
PROVEAN	Uncertain	-2.9	D;.;D
REVEL	Pathogenic	0.91
Sift	Pathogenic	0.0	D;.;D
Sift4G	Pathogenic	0.0	D;.;D
Polyphen		1.0	D;D;D
Vest4		0.84
MutPred		0.90		Loss of ubiquitination at K174 (P = 0.0309);Loss of ubiquitination at K174 (P = 0.0309);Loss of ubiquitination at K174 (P = 0.0309);
MVP		0.99
MPC		0.87
ClinPred		1.0	D
GERP RS		4.6
Varity_R		0.96
gMVP		0.99

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

Other links and lift over

dbSNP: rs28937877; hg19: chr16-75513206;