rs200077305

Variant names:

• chrX-135287348-C-A
• NM_007131.5:c.1322G>T

Your query was ambiguous. Multiple possible variants found:

• chrX-135287348-C-A
• chrX-135287348-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_007131.5(ZNF75D):​c.1322G>T​(p.Arg441Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 24)
• Consequence: ZNF75D NM_007131.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.57

Genes affected

ZNF75D (HGNC:13145): (zinc finger protein 75D) This gene encodes a protein that likely functions as a transcription factor. The protein, which belongs to the ZNF75 family, includes an N-terminal SCAN domain, a KRAB box, and five C2H2-type zinc finger motifs. Another functional gene belonging to this family is located on chromosome 16, while pseudogenes have been identified on chromosomes 11 and 12. Alternative splicing results in multiple transcripts variants. [provided by RefSeq, Jun 2010]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF75D	NM_007131.5	c.1322G>T	p.Arg441Ile	missense_variant	Exon 7 of 7	ENST00000370766.8	NP_009062.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF75D	ENST00000370766.8	c.1322G>T	p.Arg441Ile	missense_variant	Exon 7 of 7	1	NM_007131.5	ENSP00000359802.3
ZNF75D	ENST00000469456.1	n.1094G>T		non_coding_transcript_exon_variant	Exon 2 of 2	1
ZNF75D	ENST00000370764.1	c.1037G>T	p.Arg346Ile	missense_variant	Exon 4 of 4	2		ENSP00000359800.1
ZNF75D	ENST00000494295.1	n.828-31571G>T		intron_variant	Intron 1 of 3	2

Frequencies

GnomAD3 genomes Cov.: 24

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 24

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.85
BayesDel_addAF	Benign	-0.24	T
BayesDel_noAF	Benign	-0.59
CADD	Uncertain	23
DANN	Uncertain	0.97
DEOGEN2	Benign	0.30	T;.
FATHMM_MKL	Benign	0.0036	N
LIST_S2	Benign	0.39	T;T
M_CAP	Benign	0.0011	T
MetaRNN	Uncertain	0.52	D;D
MetaSVM	Benign	-0.94	T
MutationAssessor	Benign	1.9	L;.
PrimateAI	Uncertain	0.66	T
PROVEAN	Pathogenic	-7.5	D;D
REVEL	Benign	0.11
Sift	Uncertain	0.0010	D;D
Sift4G	Pathogenic	0.0010	D;D
Polyphen		0.052	B;.
Vest4		0.30
MutPred		0.80		Loss of disorder (P = 0.0299);.;
MVP		0.82
MPC		0.79
ClinPred		1.0	D
GERP RS		-0.17
Varity_R		0.65
gMVP		0.18

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chrX-134421280; COSMIC: COSV100883635;