rs201351395
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Likely benign. The variant received -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_007059.4(KPTN):c.1035G>C(p.Ser345Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,460,898 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. S345S) has been classified as Likely benign.
Frequency
Genomes: not found (cov: 27)
Exomes 𝑓: 0.0000014 ( 0 hom. )
Consequence
KPTN
NM_007059.4 synonymous
NM_007059.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -4.33
Publications
0 publications found
Genes affected
KPTN (HGNC:6404): (kaptin, actin binding protein) This gene encodes a filamentous-actin-associated protein, which is involved in actin dynamics and plays an important role in neuromorphogenesis. This protein is part of the KICSTOR protein complex that localizes to lysosomes. Mutations in this gene result in an autosomal recessive form of intellectual disability. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jul 2017]
KPTN Gene-Disease associations (from GenCC):
- macrocephaly-developmental delay syndromeInheritance: AR Classification: STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Orphanet
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BP6
Variant 19-47476679-C-G is Benign according to our data. Variant chr19-47476679-C-G is described in ClinVar as Likely_benign. ClinVar VariationId is 1145264.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-4.33 with no splicing effect.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| KPTN | NM_007059.4 | c.1035G>C | p.Ser345Ser | synonymous_variant | Exon 11 of 12 | ENST00000338134.8 | NP_008990.2 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| KPTN | ENST00000338134.8 | c.1035G>C | p.Ser345Ser | synonymous_variant | Exon 11 of 12 | 1 | NM_007059.4 | ENSP00000337850.2 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
27
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1460898Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 726642 show subpopulations
GnomAD4 exome
AF:
AC:
2
AN:
1460898
Hom.:
Cov.:
31
AF XY:
AC XY:
2
AN XY:
726642
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33474
American (AMR)
AF:
AC:
0
AN:
44582
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26094
East Asian (EAS)
AF:
AC:
0
AN:
39672
South Asian (SAS)
AF:
AC:
1
AN:
86064
European-Finnish (FIN)
AF:
AC:
0
AN:
53280
Middle Eastern (MID)
AF:
AC:
0
AN:
5766
European-Non Finnish (NFE)
AF:
AC:
1
AN:
1111622
Other (OTH)
AF:
AC:
0
AN:
60344
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.550
Heterozygous variant carriers
0
0
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1
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2
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0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
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<30
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>80
Age
GnomAD4 genome
GnomAD4 genome
Cov.:
27
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Macrocephaly-developmental delay syndrome Benign:1
Feb 17, 2020
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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