NM_014956.5(CEP164):c.3739C>T (p.Gln1247Ter) AND Nephronophthisis 15

Germline classification:: Pathogenic/Likely pathogenic (2 submissions)
Last evaluated:: Oct 22, 2024
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV001069563.9

Allele description [Variation Report for NM_014956.5(CEP164):c.3739C>T (p.Gln1247Ter)]

NM_014956.5(CEP164):c.3739C>T (p.Gln1247Ter)

Gene:

CEP164:centrosomal protein 164 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

11q23.3

Genomic location:

Preferred name:

NM_014956.5(CEP164):c.3739C>T (p.Gln1247Ter)

HGVS:

NC_000011.10:g.117409019C>T
NG_033032.1:g.92242C>T
NM_001271933.2:c.3733+15C>T
NM_014956.5:c.3739C>TMANE SELECT
NP_055771.4:p.Gln1247Ter
NC_000011.9:g.117279735C>T
NM_014956.4:c.3739C>T

Protein change:

Q1247*

Links:

dbSNP: rs140611214

NCBI 1000 Genomes Browser:

rs140611214

Molecular consequence:

NM_001271933.2:c.3733+15C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_014956.5:c.3739C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:: Nephronophthisis 15 (NPHP15)
Identifiers:: MONDO: MONDO:0013917; MedGen: C3541853; Orphanet: 3156; OMIM: 614845

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001234739	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Oct 22, 2024)	germline	clinical testing	PubMed (6) [See all records that cite these PMIDs] 22863007, 28125082, 32367404, 34132027, 34499853, 28492532
SCV002809773	Fulgent Genetics, Fulgent Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Dec 27, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001234739

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Oct 22, 2024)

germline

clinical testing

PubMed (6)
[See all records that cite these PMIDs]

SCV002809773

Fulgent Genetics, Fulgent Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Dec 27, 2023)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Exome capture reveals ZNF423 and CEP164 mutations, linking renal ciliopathies to DNA damage response signaling.

Chaki M, Airik R, Ghosh AK, Giles RH, Chen R, Slaats GG, Wang H, Hurd TW, Zhou W, Cluckey A, Gee HY, Ramaswami G, Hong CJ, Hamilton BA, Cervenka I, Ganji RS, Bryja V, Arts HH, van Reeuwijk J, Oud MM, Letteboer SJ, Roepman R, et al.

Cell. 2012 Aug 3;150(3):533-48. doi: 10.1016/j.cell.2012.06.028.

PubMed [citation]

PMID:: 22863007
PMCID:: PMC3433835

Molecular genetic findings and clinical correlations in 100 patients with Joubert syndrome and related disorders prospectively evaluated at a single center.

Vilboux T, Doherty DA, Glass IA, Parisi MA, Phelps IG, Cullinane AR, Zein W, Brooks BP, Heller T, Soldatos A, Oden NL, Yildirimli D, Vemulapalli M, Mullikin JC, Nisc Comparative Sequencing Program, Malicdan MCV, Gahl WA, Gunay-Aygun M.

Genet Med. 2017 Aug;19(8):875-882. doi: 10.1038/gim.2016.204. Epub 2017 Jan 26.

PubMed [citation]

PMID:: 28125082
PMCID:: PMC11528337

See all PubMed Citations (7)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001234739.6

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (6)

Description

This sequence change creates a premature translational stop signal (p.Gln1247*) in the CEP164 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in CEP164 are known to be pathogenic (PMID: 22863007, 28125082, 32367404, 34132027, 34499853). This variant is present in population databases (rs140611214, gnomAD 0.06%). This variant has not been reported in the literature in individuals affected with CEP164-related conditions. ClinVar contains an entry for this variant (Variation ID: 862771). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Fulgent Genetics, Fulgent Genetics, SCV002809773.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: May 16, 2025

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