NM_004187.5:c.3118C>T

Variant names:

• chrX-53195918-G-A
• rs782246658
• NM_004187.5:c.3118C>T

Variant summary

Our verdict is Pathogenic. The variant received 13 ACMG points: 13P and 0B. PVS1 PM2 PP3 PP5_Moderate

The NM_004187.5(KDM5C):​c.3118C>T​(p.Gln1040*) variant causes a stop gained, splice region 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. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Pathogenic (★). Synonymous variant affecting the same amino acid position (i.e. Q1040Q) has been classified as Uncertain significance. Variant results in nonsense mediated mRNA decay.

• Frequency: Genomes: not found (cov: 24)
• Consequence: KDM5C NM_004187.5 stop_gained, splice_region
• Scores: Splicing: ADA: 0.9981
• Clinical Significance: Pathogenic criteria provided, single submitter P:1
• Conservation: PhyloP100: 9.97
• Publications: 2 publications found

Genes affected

KDM5C (HGNC:11114): (lysine demethylase 5C) This gene is a member of the SMCY homolog family and encodes a protein with one ARID domain, one JmjC domain, one JmjN domain and two PHD-type zinc fingers. The DNA-binding motifs suggest this protein is involved in the regulation of transcription and chromatin remodeling. Mutations in this gene have been associated with X-linked cognitive disability. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2009]

KDM5C Gene-Disease associations (from GenCC):

• syndromic X-linked intellectual disability Claes-Jensen type

  Inheritance: XL Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Ambry Genetics, G2P, Labcorp Genetics (formerly Invitae), Orphanet
• X-linked syndromic intellectual disability

  Inheritance: XL Classification: DEFINITIVE Submitted by: ClinGen

ACMG classification

Our verdict: Pathogenic. The variant received 13 ACMG points.

• PVS1: Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
• PM2: Very rare variant in population databases, with high coverage
• PP3: Splicing predictors support a deleterious effect. Scorers claiming Pathogenic: dbscSNV1_ADA, dbscSNV1_RF. No scorers claiming Uncertain. Scorers claiming Benign: max_spliceai.
• PP5: Variant X-53195918-G-A is Pathogenic according to our data. Variant chrX-53195918-G-A is described in CliVar as Pathogenic. Clinvar id is 211249.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-53195918-G-A is described in CliVar as Pathogenic. Clinvar id is 211249.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-53195918-G-A is described in CliVar as Pathogenic. Clinvar id is 211249.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-53195918-G-A is described in CliVar as Pathogenic. Clinvar id is 211249.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-53195918-G-A is described in CliVar as Pathogenic. Clinvar id is 211249.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-53195918-G-A is described in CliVar as Pathogenic. Clinvar id is 211249.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-53195918-G-A is described in CliVar as Pathogenic. Clinvar id is 211249.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-53195918-G-A is described in CliVar as Pathogenic. Clinvar id is 211249.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-53195918-G-A is described in CliVar as Pathogenic. Clinvar id is 211249.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-53195918-G-A is described in CliVar as Pathogenic. Clinvar id is 211249.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-53195918-G-A is described in CliVar as Pathogenic. Clinvar id is 211249.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-53195918-G-A is described in CliVar as Pathogenic. Clinvar id is 211249.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-53195918-G-A is described in CliVar as Pathogenic. Clinvar id is 211249.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-53195918-G-A is described in CliVar as Pathogenic. Clinvar id is 211249.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-53195918-G-A is described in CliVar as Pathogenic. Clinvar id is 211249.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-53195918-G-A is described in CliVar as Pathogenic. Clinvar id is 211249.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-53195918-G-A is described in CliVar as Pathogenic. Clinvar id is 211249.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-53195918-G-A is described in CliVar as Pathogenic. Clinvar id is 211249.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-53195918-G-A is described in CliVar as Pathogenic. Clinvar id is 211249.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-53195918-G-A is described in CliVar as Pathogenic. Clinvar id is 211249.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-53195918-G-A is described in CliVar as Pathogenic. Clinvar id is 211249.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-53195918-G-A is described in CliVar as Pathogenic. Clinvar id is 211249.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-53195918-G-A is described in CliVar as Pathogenic. Clinvar id is 211249.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-53195918-G-A is described in CliVar as Pathogenic. Clinvar id is 211249.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-53195918-G-A is described in CliVar as Pathogenic. Clinvar id is 211249.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KDM5C	NM_004187.5	c.3118C>T	p.Gln1040*	stop_gained, splice_region_variant	Exon 20 of 26	ENST00000375401.8	NP_004178.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KDM5C	ENST00000375401.8	c.3118C>T	p.Gln1040*	stop_gained, splice_region_variant	Exon 20 of 26	1	NM_004187.5	ENSP00000364550.4

Frequencies

GnomAD3 genomes Cov.: 24

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 24

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: criteria provided, single submitter

Submissions by phenotype

Syndromic X-linked intellectual disability Claes-Jensen type Pathogenic:1

Sep 11, 2014

Genetic Services Laboratory, University of Chicago

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.74	D
BayesDel_noAF	Pathogenic	0.57
CADD	Pathogenic	42
DANN	Uncertain	1.0
FATHMM_MKL	Pathogenic	0.99	D
PhyloP100		10
Vest4		0.93
GERP RS		4.9
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Mutation Taster		=0/200	disease causing (ClinVar)

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.90
SpliceAI score (max)		0.010		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: rs782246658; hg19: chrX-53225100;