Is DST p.Phe35del (c.98TCT[2]) pathogenic?

DST p.Phe35del (c.98TCT[2]) is classified Uncertain significance in DST (ClinVar, Single submitter, 1 submitter; last evaluated 2020-12-14). Very rare (popmax 0.00455%, eas); Associated with Inborn genetic diseases.

What condition is associated with DST p.Phe35del (c.98TCT[2])?

DST p.Phe35del (c.98TCT[2]) is associated with Inborn genetic diseases (ClinVar).

How common is DST p.Phe35del (c.98TCT[2]) in the general population?

DST p.Phe35del (c.98TCT[2]) is very rare (popmax 0.00455%, eas) (gnomAD).

DST p.Phe35del

c.98TCT[2] · rs777785647 · VCV1773848

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00455%, eas)

Conditions

Inborn genetic diseases

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 7.6	GERP 1.2, phastCons 1
Overall
CADD	18.56	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00455% East Asian · 1/21,968 alleles

Filtering AF 0.000377% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000141%

Overall 0.000658% 9/1,367,438 alleles · very rare exomes 8/1,215,290 · genomes 1/152,148 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.00455%	21,968
South Asian	0.00227%	44,016
European (non-Finnish)	0.000587%	170,307

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: DST
Protein: p.Phe35del
Coding: c.98TCT[2]
MANE Select: NM_001374736
dbSNP: rs777785647
Type: Microsatellite
Location: chr6:56954482 (GRCh38)
Gene constraint: LOEUF 0.297 · pLI 1.00 (gnomAD)
Residue 35: the calponin-homology (ch) 1 domain; the 'actin-binding' region

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

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

DST p.Phe35Cys Uncertain significance ★ same residue
DST p.His35Arg Uncertain significance ★ same residue
DST p.His35Leu Uncertain significance ★ same residue
DST p.Gln4023Ter Pathogenic/Likely pathogenic ★★ same condition
DST c.16770+5T>C Uncertain significance ★★ same condition
DST c.17269-3T>A Uncertain significance ★★ same condition
DST c.18129+3A>G Uncertain significance ★★ same condition
DST c.182-5C>T Uncertain significance ★★ same condition

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/dst-p-phe35del (accessed [today's date]).

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