Is SDCCAG8 p.Pro93= (c.279G>A) pathogenic?

SDCCAG8 p.Pro93= (c.279G>A) is classified Benign/Likely benign in SDCCAG8 (ClinVar, Multiple submitters, 10 submitters; last evaluated 2026-02-01). Rare (popmax 0.831%, sas); Associated with Senior-Loken syndrome 7.

What condition is associated with SDCCAG8 p.Pro93= (c.279G>A)?

SDCCAG8 p.Pro93= (c.279G>A) is associated with Senior-Loken syndrome 7, Bardet-Biedl syndrome 16 (ClinVar).

How common is SDCCAG8 p.Pro93= (c.279G>A) in the general population?

SDCCAG8 p.Pro93= (c.279G>A) is rare (popmax 0.831%, sas) (gnomAD).

How is Senior-Loken syndrome inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

SDCCAG8 p.Pro93=

c.279G>A · rs145877279 · VCV260011

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 10 submitters

gnomAD v4.1

Rare

rare (popmax 0.831%, sas)

Conditions

Senior-Loken syndrome 7

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 0.22	GERP -1.8
Overall
CADD	8.619	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.831% South Asian · 757/91,066 alleles

Filtering AF 0.782% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.763%

Overall 0.207% 3,332/1,612,954 alleles · rare exomes 3,119/1,460,826 · genomes 213/152,128 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.831%	120
Middle Eastern	0.248%	404
European (non-Finnish)	0.196%	510
Admixed American	0.148%	674
Remaining individualsnot grpmax-eligible	0.146%	686
Finnishnot grpmax-eligible	0.036%	2,782
African / African-American	0.0334%	2,998
East Asian	0.0313%	3,198
Ashkenazi Jewishnot grpmax-eligible	0.0237%	4,227

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: SDCCAG8
Protein: p.Pro93=
Coding: c.279G>A
MANE Select: NM_006642
dbSNP: rs145877279
Type: single nucleotide variant
Location: chr1:243271036 (GRCh38)
Gene constraint: LOEUF 0.843 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 78.67
Residue 93: the 'disordered' region

Full SDCCAG8 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Senior-Loken syndrome 7 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: Bardet-Biedl syndrome 16

For Senior-Loken syndrome (Orphanet):

Inheritance: Autosomal recessive
Onset: Adolescent, Adult, Childhood, Infancy
Prevalence: 1-9 / 1 000 000 (Worldwide)

Similar variants

SDCCAG8 p.Pro93Leu Conflicting classifications of pathogenicity ★ ⚠ same residue
SDCCAG8 p.Pro93Ser Uncertain significance ★ ⚠ same residue
SDCCAG8 c.1356+1G>C Likely pathogenic ★★ same condition
SDCCAG8 c.221-2A>G Pathogenic ★★ same condition
SDCCAG8 c.420+1G>C Likely pathogenic ★★ same condition
SDCCAG8 c.546+1G>A Likely pathogenic ★★ same condition
SDCCAG8 c.740+356C>T Pathogenic/Likely pathogenic ★★ same condition
SDCCAG8 p.Arg374Ter 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/sdccag8-p-pro93 (accessed [today's date]).

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