chr11-94178393-T-C

Variant names:

• chr11-94178393-T-C
• rs139198736
• NM_015368.4:c.346T>C

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_015368.4(PANX1):​c.346T>C​(p.Phe116Leu) 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. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: PANX1 NM_015368.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.607

Genes affected

PANX1 (HGNC:8599): (pannexin 1) The protein encoded by this gene belongs to the innexin family. Innexin family members are the structural components of gap junctions. This protein and pannexin 2 are abundantly expressed in central nerve system (CNS) and are coexpressed in various neuronal populations. Studies in Xenopus oocytes suggest that this protein alone and in combination with pannexin 2 may form cell type-specific gap junctions with distinct properties. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.052937716).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PANX1	NM_015368.4	c.346T>C	p.Phe116Leu	missense_variant	Exon 3 of 5	ENST00000227638.8	NP_056183.2
PANX1	XM_011542734.3	c.-81T>C		5_prime_UTR_variant	Exon 4 of 6		XP_011541036.1
PANX1	XM_047426702.1	c.-81T>C		5_prime_UTR_variant	Exon 3 of 5		XP_047282658.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PANX1	ENST00000227638.8	c.346T>C	p.Phe116Leu	missense_variant	Exon 3 of 5	1	NM_015368.4	ENSP00000227638.3
PANX1	ENST00000436171.2	c.346T>C	p.Phe116Leu	missense_variant	Exon 3 of 5	1		ENSP00000411461.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.32
BayesDel_addAF	Benign	-0.31	T
BayesDel_noAF	Benign	-0.68
CADD	Benign	6.6
DANN	Benign	0.30
DEOGEN2	Benign	0.026	T;.
Eigen	Benign	-1.3
Eigen_PC	Benign	-1.3
FATHMM_MKL	Benign	0.16	N
LIST_S2	Benign	0.79	T;T
M_CAP	Benign	0.0054	T
MetaRNN	Benign	0.053	T;T
MetaSVM	Benign	-0.98	T
MutationAssessor	Benign	-1.1	N;N
PrimateAI	Benign	0.40	T
PROVEAN	Benign	-0.16	N;N
REVEL	Benign	0.034
Sift	Benign	0.96	T;T
Sift4G	Benign	0.53	T;T
Polyphen		0.0	B;B
Vest4		0.13
MutPred		0.39		Gain of catalytic residue at F116 (P = 0.0515);Gain of catalytic residue at F116 (P = 0.0515);
MVP		0.099
MPC		0.096
ClinPred		0.069	T
GERP RS		0.18
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.6
Varity_R		0.16
gMVP		0.48

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: rs139198736; hg19: chr11-93911559;