rs587777012

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001312909.2(FAM111A):​c.1531T>C​(p.Tyr511His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

Frequency

Genomes: not found (cov: 32)

Consequence

FAM111A
NM_001312909.2 missense

Scores

1
3
15

Clinical Significance

Conflicting classifications of pathogenicity no assertion criteria provided P:1U:1

Conservation

PhyloP100: -0.0890
Variant links:
Genes affected
FAM111A (HGNC:24725): (FAM111 trypsin like peptidase A) The protein encoded by this gene is cell-cycle regulated, and has nuclear localization. The C-terminal half of the protein shares homology with trypsin-like peptidases and it contains a PCNA-interacting peptide (PIP) box, that is necessary for its co-localization with proliferating cell nuclear antigen (PCNA). Reduced expression of this gene resulted in DNA replication defects, consistent with the demonstrated role for this gene in Simian Virus 40 (SV40) viral replication. Mutations in this gene have been associated with Kenny-Caffey syndrome (KCS) type 2 and the more severe osteocraniostenosis (OCS, also known as Gracile Bone Dysplasia), both characterized by short stature, hypoparathyroidism, bone development abnormalities, and hypocalcemia. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2015]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
FAM111ANM_001312909.2 linkuse as main transcriptc.1531T>C p.Tyr511His missense_variant 6/6 ENST00000675163.1 NP_001299838.1 Q96PZ2A0A024R4Z3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
FAM111AENST00000675163.1 linkuse as main transcriptc.1531T>C p.Tyr511His missense_variant 6/6 NM_001312909.2 ENSP00000501952.1 Q96PZ2

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
33
GnomAD4 genome
Cov.:
32

ClinVar

Significance: Conflicting classifications of pathogenicity
Submissions summary: Pathogenic:1Uncertain:1
Revision: no assertion criteria provided
LINK: link

Submissions by phenotype

Autosomal dominant Kenny-Caffey syndrome Pathogenic:1Uncertain:1
Pathogenic, no assertion criteria providedliterature onlyOMIMJun 06, 2013- -
Uncertain significance, no assertion criteria providedliterature onlyClinVar Staff, National Center for Biotechnology Information (NCBI)Jun 27, 2013- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
0.36
BayesDel_addAF
Benign
-0.061
T
BayesDel_noAF
Benign
-0.33
CADD
Benign
9.7
DANN
Benign
0.63
DEOGEN2
Uncertain
0.52
D;D;D;D;D
Eigen
Benign
-0.95
Eigen_PC
Benign
-0.98
FATHMM_MKL
Benign
0.18
N
LIST_S2
Benign
0.38
.;T;.;.;.
M_CAP
Pathogenic
0.76
D
MetaRNN
Uncertain
0.60
D;D;D;D;D
MetaSVM
Benign
-0.63
T
MutationAssessor
Benign
1.7
L;L;L;L;L
PrimateAI
Benign
0.32
T
PROVEAN
Benign
-2.0
N;N;N;N;N
REVEL
Benign
0.093
Sift
Benign
0.15
T;T;T;T;T
Sift4G
Benign
0.090
T;T;T;T;T
Polyphen
0.13
B;B;B;B;B
Vest4
0.75
MutPred
0.32
Loss of phosphorylation at Y511 (P = 0.0075);Loss of phosphorylation at Y511 (P = 0.0075);Loss of phosphorylation at Y511 (P = 0.0075);Loss of phosphorylation at Y511 (P = 0.0075);Loss of phosphorylation at Y511 (P = 0.0075);
MVP
0.58
MPC
0.034
ClinPred
0.055
T
GERP RS
2.7
Varity_R
0.039
gMVP
0.56

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs587777012; hg19: chr11-58920672; API