chr8-85109594-G-C

Variant names:

• chr8-85109594-G-C
• rs886039794
• ENST00000414626.2:c.44G>C

Variant summary

Our verdict is Likely pathogenic. The variant received 8 ACMG points: 8P and 0B. PM2 PP3_Strong PP5_Moderate

The ENST00000414626.2(LRRCC1):​c.44G>C​(p.Ser15Thr) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★).

• Frequency: Genomes: not found (cov: 33)
• Consequence: LRRCC1 ENST00000414626.2 missense
• Scores: Splicing: ADA: 1.000
• Clinical Significance: Pathogenic criteria provided, single submitter P:2
• Conservation: PhyloP100: 7.17
• Publications: 1 publications found

Genes affected

LRRCC1 (HGNC:29373): (leucine rich repeat and coiled-coil centrosomal protein 1) This gene encodes a centrosomal protein that maintains the structural integrity of the centrosome and plays a key role in mitotic spindle formation. The encoded protein contains an N-terminal leucine-rich repeat domain and a C-terminal coiled-coil domain. It associates with the centrosome throughout the cell cycle and accumulates on the mitotic centrosome. [provided by RefSeq, Mar 2017]

E2F5-DT (HGNC:55393): (E2F5 divergent transcript)

ACMG classification

Our verdict: Likely_pathogenic. The variant received 8 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP3: Splicing predictors support a deleterious effect. Scorers claiming Pathogenic: dbscSNV1_ADA, dbscSNV1_RF, max_spliceai. No scorers claiming Uncertain. No scorers claiming Benign.
• PP5: Variant 8-85109594-G-C is Pathogenic according to our data. Variant chr8-85109594-G-C is described in CliVar as Pathogenic. Clinvar id is 266077.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr8-85109594-G-C is described in CliVar as Pathogenic. Clinvar id is 266077.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr8-85109594-G-C is described in CliVar as Pathogenic. Clinvar id is 266077.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr8-85109594-G-C is described in CliVar as Pathogenic. Clinvar id is 266077.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr8-85109594-G-C is described in CliVar as Pathogenic. Clinvar id is 266077.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr8-85109594-G-C is described in CliVar as Pathogenic. Clinvar id is 266077.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr8-85109594-G-C is described in CliVar as Pathogenic. Clinvar id is 266077.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr8-85109594-G-C is described in CliVar as Pathogenic. Clinvar id is 266077.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr8-85109594-G-C is described in CliVar as Pathogenic. Clinvar id is 266077.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr8-85109594-G-C is described in CliVar as Pathogenic. Clinvar id is 266077.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LRRCC1	NM_033402.5	c.105-1G>C		splice_acceptor_variant, intron_variant	Intron 1 of 18	ENST00000360375.8	NP_208325.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LRRCC1	ENST00000360375.8	c.105-1G>C		splice_acceptor_variant, intron_variant	Intron 1 of 18	1	NM_033402.5	ENSP00000353538.3

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 25

GnomAD4 genome Cov.: 33

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:2

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Pathogenic:1

Mar 29, 2024

Genomic Medicine Center of Excellence, King Faisal Specialist Hospital and Research Centre

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Joubert syndrome and related disorders Pathogenic:1

-

Genomic Medicine Center of Excellence, King Faisal Specialist Hospital and Research Centre

Significance: Likely pathogenic

Review Status: flagged submission

Collection Method: research

Loss of function, the only segregating variant in the exome, autozygosity mapping. LRRCC1, is also known as CLERC for Centrosomal leucine-rich repeat and coiled-coil containing protein because of its established role as a centrosomal protein in mitosis spindle organization (Muto et al. 2008). LRRCC1 is a centrosome protein. LOF, autozygosity mapping and no other candidate variants -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.63	D
BayesDel_noAF	Benign	-0.36
CADD	Pathogenic	34
DANN	Uncertain	1.0
Eigen	Pathogenic	1.1
Eigen_PC	Pathogenic	0.99
FATHMM_MKL	Pathogenic	1.0	D
M_CAP	Benign	0.027	D
PhyloP100		7.2
ClinPred		0.89	D
GERP RS		5.8
Mutation Taster		=4/96	disease causing (ClinVar)

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.93
SpliceAI score (max)		0.99		Details are displayed if max score is > 0.2
DS_AG_spliceai		0.81		Position offset: 9
DS_AL_spliceai		0.99		Position offset: 1

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

Other links and lift over

dbSNP: rs886039794; hg19: chr8-86021829;