Is DCT p.Asn170Ser (c.509A>G) pathogenic?

DCT p.Asn170Ser (c.509A>G) is classified Likely benign in DCT (ClinVar, Single submitter, 1 submitter; last evaluated 2017-12-28). AlphaMissense: likely benign (0.0725); Low-frequency (popmax 1.1%, afr).

How common is DCT p.Asn170Ser (c.509A>G) in the general population?

DCT p.Asn170Ser (c.509A>G) is low-frequency (popmax 1.1%, afr) (gnomAD).

What do computational predictors say about DCT p.Asn170Ser (c.509A>G)?

AlphaMissense predicts likely benign (score 0.0725) — an in-silico prediction, not a clinical call.

DCT p.Asn170Ser

c.509A>G · rs34332656 · VCV730602

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0725 · ACMG-weighted

gnomAD v4.1

Rare

low-frequency (popmax 1.1%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0725	likely benign
REVEL	0.264	benign-leaning
SaProt	LLR -7.27	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.14	GERP -2.6
Regional constraint	o/e 1.05	unconstrained · MANE · 39 kb · p 0.21 · regional, not allelic
Overall
CADD	9.086	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 1.1% African / African-American · 823/75,054 alleles

Filtering AF 1.03% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.01%

Overall 0.0699% 1,129/1,614,160 alleles · low-frequency

Ancestry group	Frequency	1 in
African / African-Americangrpmax	1.1%	91
Admixed American	0.0933%	1,072
Remaining individualsnot grpmax-eligible	0.064%	1,563
European (non-Finnish)	0.0169%	5,930
East Asian	0.00891%	11,221
South Asian	0.00769%	13,011

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.Asn170Ser
Coding: c.509A>G
MANE Select: NM_001922
dbSNP: rs34332656
Type: single nucleotide variant
Location: chr13:94468832 (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.Asn170Thr Uncertain significance ★ ⚠ same residue
DCT p.Arg233Ter Pathogenic/Likely pathogenic ★★ same type
DCT p.Arg275Gln Benign ★★ same type
DCT p.Thr114= 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

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-asn170ser (accessed [today's date]).

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