Is DHCR7 p.Pro90= (c.270A>G) pathogenic?

DHCR7 p.Pro90= (c.270A>G) is classified Likely benign in DHCR7 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-07-12). Absent from gnomAD v4.1; Associated with Smith-Lemli-Opitz syndrome.

What condition is associated with DHCR7 p.Pro90= (c.270A>G)?

DHCR7 p.Pro90= (c.270A>G) is associated with Smith-Lemli-Opitz syndrome (ClinVar).

How common is DHCR7 p.Pro90= (c.270A>G) in the general population?

DHCR7 p.Pro90= (c.270A>G) is absent from gnomAD v4.1 (gnomAD).

DHCR7 p.Pro90=

c.270A>G · rs1157478971 · VCV2742136

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

Smith-Lemli-Opitz syndrome

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 -14	GERP -3.3
Overall
CADD	0.108	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: DHCR7
Protein: p.Pro90=
Coding: c.270A>G
MANE Select: NM_001360
dbSNP: rs1157478971
Type: single nucleotide variant
Location: chr11:71444044 (GRCh38)
Gene constraint: LOEUF 1.087 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 91.64

Full DHCR7 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Smith-Lemli-Opitz syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

DHCR7 c.322-1G>A Likely pathogenic ★★ same condition
DHCR7 c.412+3A>T Likely pathogenic ★★ same condition
DHCR7 c.413-2A>G Likely pathogenic ★★ same condition
DHCR7 c.626+1G>A Likely pathogenic ★★ same condition
DHCR7 c.626+1G>T Likely pathogenic ★★ same condition
DHCR7 c.627-1G>A Likely pathogenic ★★ same condition
DHCR7 c.831+1G>T Pathogenic/Likely pathogenic ★★ same condition
DHCR7 c.831+2T>A Pathogenic/Likely pathogenic ★★ 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/dhcr7-p-pro90 (accessed [today's date]).

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