chr16-75542641-C-G

Variant names:

• chr16-75542641-C-G
• rs200799769
• NM_001077418.3:c.625G>C

Variant summary

Our verdict is Likely pathogenic. The variant received 6 ACMG points: 6P and 0B. PM2 PM5 PP3_Moderate

The NM_001077418.3(TMEM231):​c.625G>C​(p.Asp209His) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic 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. D209N) has been classified as Likely pathogenic.

• Frequency: Genomes: not found (cov: 31)
• Consequence: TMEM231 NM_001077418.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.81
• Publications: 0 publications found

Genes affected

TMEM231 (HGNC:37234): (transmembrane protein 231) This gene encodes a transmembrane protein, which is a component of the B9 complex involved in the formation of the diffusion barrier between the cilia and plasma membrane. Mutations in this gene cause Joubert syndrome (JBTS). Multiple alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jan 2013]

TMEM231 Gene-Disease associations (from GenCC):

• ciliopathy

  Inheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
• Joubert syndrome 20

  Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: G2P, Labcorp Genetics (formerly Invitae)
• Joubert syndrome with oculorenal defect

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
• Meckel syndrome

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
• orofaciodigital syndrome III

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ENSG00000260092 (HGNC:):

ACMG classification

Our verdict: Likely_pathogenic. The variant received 6 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr16-75542641-C-T is described in ClinVar as Conflicting_classifications_of_pathogenicity. ClinVar VariationId is 39822.
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.905

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TMEM231	NM_001077418.3	c.625G>C	p.Asp209His	missense_variant	Exon 5 of 7	ENST00000258173.11	NP_001070886.1
TMEM231	NM_001077416.2	c.784G>C	p.Asp262His	missense_variant	Exon 4 of 6		NP_001070884.2
TMEM231	NR_074083.2	n.791G>C		non_coding_transcript_exon_variant	Exon 5 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TMEM231	ENST00000258173.11	c.625G>C	p.Asp209His	missense_variant	Exon 5 of 7	1	NM_001077418.3	ENSP00000258173.5
TMEM231	ENST00000568377.5	c.712G>C	p.Asp238His	missense_variant	Exon 4 of 6	1		ENSP00000476267.1
TMEM231	ENST00000565067.5	c.481G>C	p.Asp161His	missense_variant	Exon 4 of 6	5		ENSP00000457254.1
ENSG00000260092	ENST00000460606.1	n.118G>C		non_coding_transcript_exon_variant	Exon 2 of 5	1		ENSP00000457544.1
TMEM231	ENST00000562410.5	n.*427G>C		non_coding_transcript_exon_variant	Exon 5 of 7	1		ENSP00000454582.1
TMEM231	ENST00000570006.5	n.*5G>C		non_coding_transcript_exon_variant	Exon 5 of 7	5		ENSP00000455520.1
TMEM231	ENST00000562410.5	n.*427G>C		3_prime_UTR_variant	Exon 5 of 7	1		ENSP00000454582.1
TMEM231	ENST00000570006.5	n.*5G>C		3_prime_UTR_variant	Exon 5 of 7	5		ENSP00000455520.1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.31
BayesDel_addAF	Uncertain	0.015	T
BayesDel_noAF	Benign	-0.22
CADD	Uncertain	24
DANN	Uncertain	0.99
DEOGEN2	Uncertain	0.47	T;.;D
Eigen	Benign	0.078
Eigen_PC	Benign	-0.049
FATHMM_MKL	Uncertain	0.92	D
LIST_S2	Uncertain	0.89	D;D;D
M_CAP	Benign	0.073	D
MetaRNN	Pathogenic	0.91	D;D;D
MetaSVM	Benign	-0.43	T
MutationAssessor	Uncertain	2.3	M;.;.
PhyloP100		3.8
PrimateAI	Uncertain	0.57	T
PROVEAN	Uncertain	-3.2	D;.;D
REVEL	Uncertain	0.39
Sift	Uncertain	0.0050	D;.;D
Sift4G	Uncertain	0.0090	D;D;D
Polyphen		0.99	D;.;.
Vest4		0.76
MutPred		0.77		Gain of helix (P = 0.062);.;.;
MVP		0.50
MPC		0.045
ClinPred		0.97	D
GERP RS		2.3
Varity_R		0.20
gMVP		0.63
Mutation Taster		=71/29	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.050		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: rs200799769; hg19: chr16-75576539;