MutationT@ster 2025

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Input seems to be ok - now mapping the variant to the different transcripts...
Querying Taster for transcript #1: ENST00000367435
Querying Taster for transcript #2: ENST00000635846
MT speed 0.83 s - this script 3.332739 s

Transcript summary:

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Transcript	Gene symbol	Prediction	Tree vote	Model	Prediction problem	Splice site change	Known ClinVar disease mutation	Potential ClinVar disease mutation	Amino acid changes	Variant type	dbSNP ID	Protein length	Features at a glance
ENST00000635846	CDC73	Deleterious	10\|0	complex_aae		No	Yes		R234*	Single base exchange		NMD	Amino acid sequence changed Known disease mutation: ClinVar ID 988553 (pathogenic) NMD
ENST00000367435(MANE Select)	CDC73	Deleterious	10\|0	complex_aae		No	Yes		R234*	Single base exchange		NMD	Amino acid sequence changed Known disease mutation: ClinVar ID 988553 (pathogenic) NMD Protein features (might be) affected

MutationT@ster 2025

Variant:

1:193142037C>T_2_ENST00000635846

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Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Known disease mutation: ClinVar ID 988553 (pathogenic)
NMD

Model: complex_aae
Tree vote: 10|0 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr1:193142037C>T (GRCh38)

Gene symbol

CDC73

Gene constraints

LOEUF: 0.42, LOF (oe): 0.24, misssense (oe): 0.49, synonymous (oe): 0.91 ? (gnomAD)

Ensembl transcript ID

ENST00000635846.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.700C>T
g.20055C>T

AA changes

R234* Score: 6.0?

Frameshift

No

Length of protein

NMD

Pathogenic variant (ClinVar)

Hereditary cancer-predisposing syndrome
Parathyroid carcinoma

pathogenic

ClinVar OMIM

Variant DBs

dbSNP ID	rs1675915231
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	0	1	1

Protein conservation

Species	Match	AA	Alignment
Human		234	D	I	V	S	R	E	R	V	W	R	T	R	T	T	I	L	Q	S	T	G	K	E	G	A	S	A	R	K	T	Q	T	P	A	A	Q	P	V	P	R
mutated	partly conserved	34	DE	V	I	F	G	E	F	S	W	P	K	N	V	KTNY	V	V	W	G	T	G	K	E	G
Ptroglodytes	no homologue
Mmulatta	no homologue
Fcatus	no homologue
Mmusculus	no homologue
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.777	0.998
	2.322	1
(flanking)	9.754	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

1

Strand

1

Original gDNA sequence snippet

GAGAGAGAGTATGGAGGACACGAACAACTATCTTACAAAGC

Altered gDNA sequence snippet

GAGAGAGAGTATGGAGGACATGAACAACTATCTTACAAAGC

Original cDNA sequence snippet

GAGAGAGAGTATGGAGGACACGAACAACTATCTTACAAAGC

Altered cDNA sequence snippet

GAGAGAGAGTATGGAGGACATGAACAACTATCTTACAAAGC

Wildtype AA sequence

MADVLSVLRQ YNIQKKEIVV KGDEVIFGEF SWPKNVKTNY VVWGTGKEGQ PREYYTLDSI
LFLLNNVHLS HPVYVRRAAT ENIPVVRRPD RKDLLGYLNG EASTSASIDR SAPLEIGLQR
STQVKRAADE VLAEAKKPRI EDEECVRLDK ERLAARLEGH KEGIVQTEQI RSLSEAMSVE
KIAAIKAKIM AKKRSTIKTD LDDDITALKQ RSFVDAEVDV TRDIVSRERV WRTRTTILQS
TGKEGASARK TQTPAAQPVP RPVSQARPPP NQKKGSRTPI IIIPAATTSL ITMLNAKDLL
QDLKFVPSDE KKKQGCQREN ETLIQRRKDQ MQPGGTAISV TVPYRVVDQP LKLMPQDWDR
VVAVFVQGPA WQFKGWPWLL PDGSPVDIFA KIKAFHLKYD EVRLDPNVQK WDVTVLELSY
HKRHLDRPVF LRFWETLDRY MVKHKSHLRF *

Mutated AA sequence

MADVLSVLRQ YNIQKKEIVV KGDEVIFGEF SWPKNVKTNY VVWGTGKEGQ PREYYTLDSI
LFLLNNVHLS HPVYVRRAAT ENIPVVRRPD RKDLLGYLNG EASTSASIDR SAPLEIGLQR
STQVKRAADE VLAEAKKPRI EDEECVRLDK ERLAARLEGH KEGIVQTEQI RSLSEAMSVE
KIAAIKAKIM AKKRSTIKTD LDDDITALKQ RSFVDAEVDV TRDIVSRERV WRT*

Position of stopcodon in wt / mu CDS

1353 / 702

Position (AA) of stopcodon in wt / mu AA sequence

451 / 234

Position of stopcodon in wt / mu cDNA

1374 / 723

Position of start ATG in wt / mu cDNA

22 / 22

Last intron/exon boundary

1337

Theoretical NMD boundary in CDS

1265

Length of CDS

1353

Coding sequence (CDS) position

700

cDNA position

721

gDNA position

20055

Chromosomal position

193142037

Speed

0.41 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

Back to summary table

MutationT@ster 2025

Variant:

1:193142037C>T_1_ENST00000367435

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Known disease mutation: ClinVar ID 988553 (pathogenic)
NMD
Protein features (might be) affected

Model: complex_aae
Tree vote: 10|0 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr1:193142037C>T (GRCh38)

Gene symbol

CDC73

Gene constraints

LOEUF: 0.42, LOF (oe): 0.24, misssense (oe): 0.49, synonymous (oe): 0.91 ? (gnomAD)

Ensembl transcript ID

ENST00000367435.5

Genbank transcript ID

NM_024529 (exact from MANE)

UniProt / AlphaMissense peptide

CDC73_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.700C>T
g.20055C>T

AA changes

R234* Score: 6.0?

Frameshift

No

Length of protein

NMD

Pathogenic variant (ClinVar)

Hereditary cancer-predisposing syndrome
Parathyroid carcinoma

pathogenic

ClinVar OMIM

Variant DBs

dbSNP ID	rs1675915231
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	0	1	1

Protein conservation

Species	Match	AA	Alignment
Human		234	D	I	V	S	R	E	R	V	W	R	T	R	T	T	I	L	Q	S	T	G	K	N	F	S	K	N	I	F	A	I	L	Q	S	V	K	A	R	E	E	G	R	A	P	E	Q	R	P	A	P	N	A	A	P	V	D	P	T	L	R	T	K	Q	P	I	P	A	A	Y	N	R	Y	D	Q	E	R	F	K	G	K	E	E	T	E	G	F	K	I	D	T	M	G	T	Y
mutated	no alignment	n/a
Ptroglodytes	all identical	234	D	I	V	S	R	E	R	V	W	R	T	R	T	T	I	L	Q	S	T	G	K	N	F	S	K	N	I	F	A	I	L	Q	S	V	K	A	R	E	E	G	R	A	P	E	Q	R	P	A	P	N	A	A	P	V	D	P	T	L	R	T	K	Q	P	I	P	A	A	Y	N	R	Y	D	Q	E	R	F	K	G
Mmulatta	all identical	234	D	I	V	S	R	E	R	V	W	R	T	R	T	T	I	L	Q	S	T	G	K	N	F	S	K	N	I	F	A	I	L	Q	S	V	K	A	R	E	E	G	R	A	P	E	Q	R	P	A	P	N	A	A	P	V	D	P	T	L	R	T	K	Q	P	I	P	A	A	Y	N	R	Y	D	Q	E	R	F	K	G
Fcatus	all identical	234	D	I	V	S	R	E	R	V	W	R	T	R	T	T	I	L	Q	S	T	G	K	N	F	S	K	N	I	F	A	I	L	Q	S	V	K	A	R	E	E	G	R	A	P	E	Q	R	P	A	P	N	A	A	P	V	D	P	T	L	R	T	K	Q	P	I	P	A	A	Y	N	R	Y	D	Q	E	R	F	K	G
Mmusculus	all identical	234	D	I	V	S	R	E	R	V	W	R	T	R	T	T	I	L	Q	S	T	G	K	N	F	S	K	N	I	F	A	I	L	Q	S	V	K	A	R	E	E	G	R	A	P	E	Q	R	P	A	P	N	A	A	P	V	D	P	T	L	R	T	K	Q	P	I	P	A	A	Y	N	R	Y	D	Q	E	R	F	K	G
Ggallus	partly conserved	234	D	I	V	S	R	E	R	V	W	R	T	R	T	T	I	L	Q	S	T	G	K	N	F	A	K	N	I	F	A	I	L	Q	S	V	K	A	R	E	E	G	R	A	P	E	Q	R	P	A	P	N	T	A	P	T	D	P	T	L	R	N	K	Q	P	I	P	A	A	Y	N	R	Y	D	Q	E	R	F	K	G
Trubripes	partly conserved	271	D	I	V	S	R	E	R	V	W	R	T	R	T	T	I	L	Q	S	S	G	K	N	F	S	K	N	I	F	A	I	L	Q	S	V	K	A	R	E	E	G	R	A	P	E	Q	R	P	A	Q	N	P	T	Q	P	D	V	S	L	R	N	K	Q	P	V	P	T	A	Y	N	R	Y	D	Q	E	R	F	K	G
Drerio	no homologue
Dmelanogaster	partly conserved	593	D	I	I	S	R	E	R	Q	W	R	T	R	T	S	I	L	Q	S	T	G	K	I	F	A	K	N	I	F	A	M	L	Q	G	I	K	A	R	E	E	G	R	N	R	P	Q	V	P	N	P	I	K	M	P	E	P	A	R	I	A	K	P	Q	P	Q	L	S	Q	Y	N	R	Y	D	Q
Celegans	partly conserved	228	-	-	L	P	K	T	R	I	H	K	T	R	E	N	V	M	-	-	L	G	A	R	D	L	S	N	V	L	D	I	I	T	S	A	Q	R	Q	W	D	L	N	E	K	K	E	K	-	-	-	-	V	A	A	V	H	A	T	N	L	S	K	D	Q	S	G	A	A	G	G	Q	Q	Q	R	S	G	Y	S	R	Y	A	Q
Xtropicalis	partly conserved	234	D	I	V	S	R	E	R	V	W	R	T	R	T	T	I	L	Q	S	T	G	K	N	F	A	K	N	I	F	A	I	L	Q	S	V	K	A	R	E	E	G	R	A	P	E	Q	R	P	T	Q	T	A	A	P	T	D	P	A	L	R	T	N	K	P	V	P	A	A	Y	N	R	Y	D	Q	E	R	F	K	G

Protein features

Start (aa)	End (aa)	Feature	Details
2	531	CHAIN		lost
200	250	REGION	Interaction with CTNNB1	lost
200	531	REGION	Interaction with POLR2A and PAF1	lost
235	238	HELIX		lost
247	259	HELIX		lost
260	292	REGION		lost
301	301	CROSSLNK	Glycyl lysine isopeptide (Lys-Gly)	lost
308	308	CROSSLNK	Glycyl lysine isopeptide (Lys-Gly)	lost
321	321	CROSSLNK	Glycyl lysine isopeptide (Lys-Gly)	lost
325	340	COMPBIAS	Polar residues	lost
325	358	REGION		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.777	0.998
	2.322	1
(flanking)	9.754	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

1

Strand

1

Original gDNA sequence snippet

GAGAGAGAGTATGGAGGACACGAACAACTATCTTACAAAGC

Altered gDNA sequence snippet

GAGAGAGAGTATGGAGGACATGAACAACTATCTTACAAAGC

Original cDNA sequence snippet

GAGAGAGAGTATGGAGGACACGAACAACTATCTTACAAAGC

Altered cDNA sequence snippet

GAGAGAGAGTATGGAGGACATGAACAACTATCTTACAAAGC

Wildtype AA sequence

MADVLSVLRQ YNIQKKEIVV KGDEVIFGEF SWPKNVKTNY VVWGTGKEGQ PREYYTLDSI
LFLLNNVHLS HPVYVRRAAT ENIPVVRRPD RKDLLGYLNG EASTSASIDR SAPLEIGLQR
STQVKRAADE VLAEAKKPRI EDEECVRLDK ERLAARLEGH KEGIVQTEQI RSLSEAMSVE
KIAAIKAKIM AKKRSTIKTD LDDDITALKQ RSFVDAEVDV TRDIVSRERV WRTRTTILQS
TGKNFSKNIF AILQSVKARE EGRAPEQRPA PNAAPVDPTL RTKQPIPAAY NRYDQERFKG
KEETEGFKID TMGTYHGMTL KSVTEGASAR KTQTPAAQPV PRPVSQARPP PNQKKGSRTP
IIIIPAATTS LITMLNAKDL LQDLKFVPSD EKKKQGCQRE NETLIQRRKD QMQPGGTAIS
VTVPYRVVDQ PLKLMPQDWD RVVAVFVQGP AWQFKGWPWL LPDGSPVDIF AKIKAFHLKY
DEVRLDPNVQ KWDVTVLELS YHKRHLDRPV FLRFWETLDR YMVKHKSHLR F*

Mutated AA sequence

MADVLSVLRQ YNIQKKEIVV KGDEVIFGEF SWPKNVKTNY VVWGTGKEGQ PREYYTLDSI
LFLLNNVHLS HPVYVRRAAT ENIPVVRRPD RKDLLGYLNG EASTSASIDR SAPLEIGLQR
STQVKRAADE VLAEAKKPRI EDEECVRLDK ERLAARLEGH KEGIVQTEQI RSLSEAMSVE
KIAAIKAKIM AKKRSTIKTD LDDDITALKQ RSFVDAEVDV TRDIVSRERV WRT*

Position of stopcodon in wt / mu CDS

1596 / 702

Position (AA) of stopcodon in wt / mu AA sequence

532 / 234

Position of stopcodon in wt / mu cDNA

1766 / 872

Position of start ATG in wt / mu cDNA

171 / 171

Last intron/exon boundary

1729

Theoretical NMD boundary in CDS

1508

Length of CDS

1596

Coding sequence (CDS) position

700

cDNA position

870

gDNA position

20055

Chromosomal position

193142037

Speed

0.42 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

Back to summary table