11-117409800-A-T

Variant names:

• chr11-117409800-A-T
• rs756182128
• NM_014956.5:c.3931A>T
• CEP164 p.Thr1311Ser

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_014956.5(CEP164):​c.3931A>T​(p.Thr1311Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000137 in 511,530 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Benign in ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T1311P) has been classified as Benign.

• Frequency:
  • Genomes: 𝑓 0.0 (0 hom., cov: 0)
  • Exomes 𝑓: 0.000014 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: CEP164 NM_014956.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17
• Publications: 0 publications found

Genes affected

CEP164 (HGNC:29182): (centrosomal protein 164) This gene encodes a centrosomal protein involved in microtubule organization, DNA damage response, and chromosome segregation. The encoded protein is required for assembly of primary cilia and localizes to mature centrioles. Defects in this gene are a cause of nephronophthisis-related ciliopathies. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2012]

CEP164 Gene-Disease associations (from GenCC):

• CEP164-related ciliopathy

  Inheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
• nephronophthisis 15

  Inheritance: AR Classification: DEFINITIVE, STRONG, MODERATE Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae), Laboratory for Molecular Medicine, G2P
• Senior-Loken syndrome

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.032123595).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014956.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CEP164	NM_014956.5	MANE Select	c.3931A>T	p.Thr1311Ser	missense	Exon 30 of 33	NP_055771.4
	CEP164	NM_001440949.1		c.3937A>T	p.Thr1313Ser	missense	Exon 30 of 33	NP_001427878.1
	CEP164	NM_001440950.1		c.3931A>T	p.Thr1311Ser	missense	Exon 30 of 33	NP_001427879.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CEP164	ENST00000278935.8	TSL:1 MANE Select	c.3931A>T	p.Thr1311Ser	missense	Exon 30 of 33	ENSP00000278935.3	Q9UPV0-1
	CEP164	ENST00000533223.1	TSL:1	n.4789A>T		non_coding_transcript_exon	Exon 16 of 16
	CEP164	ENST00000957770.1		c.3862A>T	p.Thr1288Ser	missense	Exon 27 of 30	ENSP00000627829.1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 0 AN: 59962 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.0000137 AC: 7 AN: 511530 Hom.: 0 Cov.: 35 AF XY: 0.0000192 AC XY: 5 AN XY: 260352

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.00 AC: 0 AN: 14346

American (AMR) AF: 0.00 AC: 0 AN: 23808

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 10578

East Asian (EAS) AF: 0.0000918 AC: 1 AN: 10898

South Asian (SAS) AF: 0.0000236 AC: 1 AN: 42408

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 25024

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2876

European-Non Finnish (NFE) AF: 0.0000138 AC: 5 AN: 361560

Other (OTH) AF: 0.00 AC: 0 AN: 20032

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.000000285107), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 59962 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 28622

African (AFR) AF: 0.00 AC: 0 AN: 16526

American (AMR) AF: 0.00 AC: 0 AN: 5156

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 1404

East Asian (EAS) AF: 0.00 AC: 0 AN: 1938

South Asian (SAS) AF: 0.00 AC: 0 AN: 1946

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 3486

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 88

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 28210

Other (OTH) AF: 0.00 AC: 0 AN: 856

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.089
BayesDel_addAF	Benign	-0.39	T
BayesDel_noAF	Benign	-0.79
CADD	Benign	0.017
DANN	Benign	0.59
DEOGEN2	Benign	0.0070	T
Eigen	Benign	-1.3
Eigen_PC	Benign	-1.3
FATHMM_MKL	Benign	0.019	N
LIST_S2	Benign	0.21	T
M_CAP	Benign	0.0058	T
MetaRNN	Benign	0.032	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	0.90	L
PhyloP100		-1.2
PrimateAI	Benign	0.26	T
PROVEAN	Benign	-0.15	N
REVEL	Benign	0.0080
Sift	Benign	0.76	T
Sift4G	Benign	0.58	T
Varity_R		0.026
gMVP		0.13
Mutation Taster		=96/4	polymorphism

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs756182128;

hg19: chr11-117280516;