4-373417-C-T

Variant names:

• chr4-373417-C-T
• rs113884485
• NM_003441.4:c.980C>T

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_003441.4(ZNF141):​c.980C>T​(p.Thr327Ile) 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 benign outcome for this variant. 14/22 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 variant affecting the same amino acid position, but resulting in a different missense (i.e. T327S) has been classified as Benign.

• Frequency: Genomes: not found (cov: 33)
• Consequence: ZNF141 NM_003441.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.32
• Publications: 9 publications found

Genes affected

ZNF141 (HGNC:12926): (zinc finger protein 141) The protein encoded by this gene is a zinc finger protein that may be a tumor suppressor. Defects in this gene have been associated with autosomal recessive postaxial polydactyly type A. [provided by RefSeq, Jan 2017]

ZNF141 Gene-Disease associations (from GenCC):

• postaxial polydactyly type A

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
• polydactyly, postaxial, type A6

  Inheritance: AR Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.1467492).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003441.4. 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
	ZNF141	NM_003441.4	MANE Select	c.980C>T	p.Thr327Ile	missense	Exon 4 of 4	NP_003432.1	Q15928
	ZNF141	NM_001348277.2		c.752C>T	p.Thr251Ile	missense	Exon 2 of 2	NP_001335206.1	Q4W5N2
	ZNF141	NM_001348278.2		c.570+410C>T		intron	N/A	NP_001335207.1	D6RIY0

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF141	ENST00000240499.8	TSL:1 MANE Select	c.980C>T	p.Thr327Ile	missense	Exon 4 of 4	ENSP00000240499.7	Q15928
	ZNF141	ENST00000512994.5	TSL:1	c.570+410C>T		intron	N/A	ENSP00000425799.1	D6RIY0
	ZNF141	ENST00000885054.1		c.1115C>T	p.Thr372Ile	missense	Exon 5 of 5	ENSP00000555113.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.24
BayesDel_addAF	Benign	-0.35	T
BayesDel_noAF	Benign	-0.74
CADD	Benign	17
DANN	Uncertain	1.0
DEOGEN2	Benign	0.14	T
Eigen	Benign	-0.46
Eigen_PC	Benign	-0.62
FATHMM_MKL	Benign	0.00010	N
LIST_S2	Benign	0.15	T
M_CAP	Benign	0.0024	T
MetaRNN	Benign	0.15	T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	0.37	N
PhyloP100		-1.3
PrimateAI	Benign	0.31	T
PROVEAN	Pathogenic	-4.4	D
REVEL	Benign	0.044
Sift	Benign	0.075	T
Sift4G	Benign	0.20	T
Polyphen		0.97	D
Vest4		0.037
MutPred		0.41		Loss of phosphorylation at T327 (P = 0.0331)
MVP		0.36
MPC		0.26
ClinPred		0.68	D
GERP RS		0.23
Varity_R		0.14
gMVP		0.014
Mutation Taster		=100/0	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

Other links and lift over

dbSNP: rs113884485; hg19: chr4-367206;