rs886039852

Positions:

• chr11-59125971-C-A

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2 PP3_Moderate

The NM_198947.4(FAM111B):​c.1874C>A​(p.Thr625Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as not provided (no stars).

• Frequency: Genomes: not found (cov: 33)
• Consequence: FAM111B NM_198947.4 missense
• Clinical Significance: not provided no classification provided O:1
• Conservation: PhyloP100: 0.627

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]

ACMG classification

Verdict is Uncertain_significance. Variant got 4 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.874

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FAM111B	NM_198947.4	c.1874C>A	p.Thr625Asn	missense_variant	4/4	ENST00000343597.4	NP_945185.1
FAM111B	NM_001142703.2	c.1784C>A	p.Thr595Asn	missense_variant	3/3		NP_001136175.1
FAM111B	NM_001142704.2	c.1784C>A	p.Thr595Asn	missense_variant	2/2		NP_001136176.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FAM111B	ENST00000343597.4	c.1874C>A	p.Thr625Asn	missense_variant	4/4	1	NM_198947.4	ENSP00000341565.3
FAM111B	ENST00000529618.5	c.1784C>A	p.Thr595Asn	missense_variant	3/3	1		ENSP00000432875.1
FAM111B	ENST00000620384.1	c.1874C>A	p.Thr625Asn	missense_variant	2/2	2		ENSP00000483456.1
FAM111B	ENST00000411426.1	c.1784C>A	p.Thr595Asn	missense_variant	2/2	4		ENSP00000393855.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 33

ClinVar

Significance: not provided

Submissions summary: Other:1

Revision: no classification provided

Submissions by phenotype

Hereditary sclerosing poikiloderma with tendon and pulmonary involvement Other:1

not provided, no classification provided

literature only

GeneReviews

-

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.29
BayesDel_addAF	Uncertain	0.041	T
BayesDel_noAF	Benign	-0.18
CADD	Benign	19
DANN	Uncertain	0.98
DEOGEN2	Uncertain	0.67	.;.;D;D
Eigen	Benign	0.15
Eigen_PC	Benign	0.0023
FATHMM_MKL	Benign	0.62	D
LIST_S2	Benign	0.52	T;.;.;T
M_CAP	Uncertain	0.16	D
MetaRNN	Pathogenic	0.87	D;D;D;D
MetaSVM	Uncertain	0.020	D
MutationAssessor	Uncertain	2.3	.;.;M;M
PrimateAI	Benign	0.46	T
PROVEAN	Uncertain	-3.7	D;D;D;.
REVEL	Uncertain	0.38
Sift	Uncertain	0.0030	D;D;D;.
Sift4G	Uncertain	0.0090	D;D;D;D
Polyphen		1.0	.;.;D;D
Vest4		0.76
MutPred		0.71		.;.;Gain of sheet (P = 0.0827);Gain of sheet (P = 0.0827);
MVP		0.82
MPC		0.36
ClinPred		0.94	D
GERP RS		2.9
Varity_R		0.33
gMVP		0.79

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

Other links and lift over

dbSNP: rs886039852; hg19: chr11-58893444;