Is DCHS1 p.Ser3067= (c.9201A>G) pathogenic?

DCHS1 p.Ser3067= (c.9201A>G) is classified Likely benign in DCHS1 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-05-30). Very rare (popmax 0.00536%, nfe); Associated with Inborn genetic diseases.

What condition is associated with DCHS1 p.Ser3067= (c.9201A>G)?

DCHS1 p.Ser3067= (c.9201A>G) is associated with Inborn genetic diseases (ClinVar).

How common is DCHS1 p.Ser3067= (c.9201A>G) in the general population?

DCHS1 p.Ser3067= (c.9201A>G) is very rare (popmax 0.00536%, nfe) (gnomAD).

DCHS1 p.Ser3067=

c.9201A>G · rs541836028 · VCV1601975

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00536%, nfe)

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 · no allele here is in the release
Constraint at this position
Conservation	phyloP -5.6	GERP -3.2
Overall
CADD	0.803	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00536% European (non-Finnish) · 62/1,156,456 alleles

Filtering AF 0.00427% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00387%

Overall 0.00445% 63/1,415,804 alleles · very rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00536%	18,653
Admixed American	0.00189%	52,826

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: DCHS1
Protein: p.Ser3067=
Coding: c.9201A>G
MANE Select: NM_003737
dbSNP: rs541836028
Type: single nucleotide variant
Location: chr11:6622475 (GRCh38)
Gene constraint: LOEUF 0.491 · pLI 0.33 · ClinGen HI 1/3 (gnomAD)
Residue 3067: the 'disordered' region

Full DCHS1 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

DCHS1 p.Ala1454Val Uncertain significance ★★ ⚠ same condition
DCHS1 p.Ala1460Pro Uncertain significance ★★ same condition
DCHS1 p.Ala1490Glu Uncertain significance ★★ ⚠ same condition
DCHS1 p.Ala1547Gly Uncertain significance ★★ ⚠ same condition
DCHS1 p.Ala1564Gly Uncertain significance ★★ ⚠ same condition
DCHS1 p.Ala1673Val Uncertain significance ★★ same condition
DCHS1 p.Ala1754Ser Uncertain significance ★★ ⚠ same condition
DCHS1 p.Ala1754Val 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/dchs1-p-ser3067 (accessed [today's date]).

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