rs886039851
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PM4_Supporting
The NM_198947.4(FAM111B):c.1262_1264del(p.Lys421del) variant causes a inframe deletion change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as not provided (no stars).
Frequency
Genomes: not found (cov: 33)
Consequence
FAM111B
NM_198947.4 inframe_deletion
NM_198947.4 inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.458
Genes affected
FAM111B (HGNC:24200): (FAM111 trypsin like peptidase B) This gene encodes a protein with a trypsin-like cysteine/serine peptidase domain in the C-terminus. Mutations in this gene are associated with an autosomal dominant form of hereditary fibrosing poikiloderma (HFP). Affected individuals display mottled pigmentation, telangiectasia, epidermal atrophy, tendon contractures, and progressive pulmonary fibrosis. Alternative splicing results in multiple transcript variants encoding distinct isoforms. A paralog of this gene which also has a trypsin‐like peptidase domain, FAM111A, is located only 16 kb from this gene on human chromosome 11q12.1. [provided by RefSeq, Apr 2014]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 3 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
PM4
?
Nonframeshift variant in NON repetitive region in NM_198947.4. Strenght limited to Supporting due to length of the change: 1aa.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FAM111B | NM_198947.4 | c.1262_1264del | p.Lys421del | inframe_deletion | 4/4 | ENST00000343597.4 | |
FAM111B | NM_001142703.2 | c.1172_1174del | p.Lys391del | inframe_deletion | 3/3 | ||
FAM111B | NM_001142704.2 | c.1172_1174del | p.Lys391del | inframe_deletion | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FAM111B | ENST00000343597.4 | c.1262_1264del | p.Lys421del | inframe_deletion | 4/4 | 1 | NM_198947.4 | P2 | |
FAM111B | ENST00000529618.5 | c.1172_1174del | p.Lys391del | inframe_deletion | 3/3 | 1 | A2 | ||
FAM111B | ENST00000411426.1 | c.1172_1174del | p.Lys391del | inframe_deletion | 2/2 | 4 | A2 | ||
FAM111B | ENST00000620384.1 | c.1262_1264del | p.Lys421del | inframe_deletion | 2/2 | 2 | P2 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 genomes
?
Cov.:
33
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? Cov.: 33
GnomAD4 genome
?
Cov.:
33
ClinVar
Significance: not provided
Submissions summary: Other:1
Revision: no classification provided
LINK: link
Submissions by phenotype
Hereditary sclerosing poikiloderma with tendon and pulmonary involvement Other:1
not provided, no classification provided | literature only | GeneReviews | - | May be associated with less severe extracutaneous phenotype. Further studies are needed. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
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