Is DCT p.Thr114= (c.342C>T) pathogenic?

DCT p.Thr114= (c.342C>T) is classified Benign in DCT (ClinVar, Multiple submitters, 2 submitters; last evaluated 2017-12-28). Low-frequency (popmax 1.9%, afr).

How common is DCT p.Thr114= (c.342C>T) in the general population?

DCT p.Thr114= (c.342C>T) is low-frequency (popmax 1.9%, afr) (gnomAD).

DCT p.Thr114=

c.342C>T · rs34723994 · VCV717314

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

low-frequency (popmax 1.9%, afr)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -13	GERP -4.2
Overall
CADD	0.072	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 1.9% African / African-American · 1,425/75,016 alleles

Filtering AF 1.82% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.78%

Overall 0.101% 1,630/1,614,052 alleles · low-frequency

Ancestry group	Frequency	1 in
African / African-Americangrpmax	1.9%	53
Middle Eastern	0.181%	551
Remaining individualsnot grpmax-eligible	0.139%	718
Admixed American	0.108%	923
South Asian	0.00659%	15,178
European (non-Finnish)	0.00305%	32,777

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: DCT
Protein: p.Thr114=
Coding: c.342C>T
MANE Select: NM_001922
dbSNP: rs34723994
Type: single nucleotide variant
Location: chr13:94468999 (GRCh38)
Gene constraint: LOEUF 1.101 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 89.33 · 1 PDB

Full DCT gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

DCT p.Arg233Ter Pathogenic/Likely pathogenic ★★ same type
DCT p.Arg275Gln Benign ★★ same type
DCT p.Arg326Ter Pathogenic ★ same type
DCT p.Trp71Ter Pathogenic ★ same type
DCT c.1180-2098C>T Uncertain significance ★ same type
DCT c.1180-2111A>G Uncertain significance ★ same type
DCT p.Ala144Thr Uncertain significance ★ ⚠ same type
DCT p.Ala206Thr Uncertain significance ★ ⚠ same type

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/dct-p-thr114 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown