Is DCXR p.Gly7= (c.21C>T) pathogenic?

DCXR p.Gly7= (c.21C>T) is classified Likely benign in DCXR (ClinVar, Single submitter, 2 submitters; last evaluated 2024-11-14). Low-frequency (popmax 2.01%, afr).

How common is DCXR p.Gly7= (c.21C>T) in the general population?

DCXR p.Gly7= (c.21C>T) is low-frequency (popmax 2.01%, afr) (gnomAD).

DCXR p.Gly7=

c.21C>T · rs191302793 · VCV3039358

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

low-frequency (popmax 2.01%, 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 -1.3	GERP -1.5
Overall
CADD	4.463	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 2.01% African / African-American · 1,506/74,884 alleles

Filtering AF 1.93% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.89%

Overall 0.108% 1,724/1,591,114 alleles · low-frequency

Ancestry group	Frequency	1 in
African / African-Americangrpmax	2.01%	50
Middle Eastern	0.252%	398
Remaining individualsnot grpmax-eligible	0.147%	681
Admixed American	0.139%	721
South Asian	0.00335%	29,893
European (non-Finnish)	0.0023%	43,570

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: DCXR
Protein: p.Gly7=
Coding: c.21C>T
MANE Select: NM_016286
dbSNP: rs191302793
Type: single nucleotide variant
Location: chr17:82037662 (GRCh38)
Gene constraint: LOEUF 1.362 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 96.19 · 3 PDB

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

Similar variants

DCXR c.53-8C>T Benign ★★ same type
DCXR c.52+1G>A Uncertain significance ★ same type
DCXR p.Ala110Val Uncertain significance ★ ⚠ same type
DCXR p.Ala155Ser Uncertain significance ★ ⚠ same type
DCXR p.Ala189Thr Uncertain significance ★ ⚠ same type
DCXR p.Ala6Val Uncertain significance ★ ⚠ same type
DCXR p.Ala87Val Uncertain significance ★ ⚠ same type
DCXR p.Ala99Thr 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/dcxr-p-gly7 (accessed [today's date]).

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