Is DSCAML1 p.Asp714= (c.2142C>T) pathogenic?

DSCAML1 p.Asp714= (c.2142C>T) is classified Likely benign in DSCAML1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-11-25). Ultra-rare (popmax 0.0318%, nfe).

How common is DSCAML1 p.Asp714= (c.2142C>T) in the general population?

DSCAML1 p.Asp714= (c.2142C>T) is ultra-rare (popmax 0.0318%, nfe) (gnomAD).

DSCAML1 p.Asp714=

c.2142C>T · rs139385882 · VCV1652895

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0318%, nfe)

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 -5.2	GERP -5.5
Overall
CADD	0.063	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0318% European (non-Finnish) · 375/1,178,164 alleles

Filtering AF 0.0291% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0281%

Overall 0.0312% 502/1,610,988 alleles · ultra-rare exomes 447/1,458,716 · genomes 55/152,272 · joint denominator

Ancestry group	Frequency	1 in
Ashkenazi Jewishnot grpmax-eligible	0.206%	485
Remaining individualsnot grpmax-eligible	0.0385%	2,600
European (non-Finnish)grpmax	0.0318%	3,142
East Asian	0.0223%	4,482
African / African-American	0.02%	5,000
Admixed American	0.0167%	5,995
Middle Eastern	0.0165%	6,048
South Asian	0.00444%	22,540
Finnishnot grpmax-eligible	0.00313%	31,982

Ashkenazi Jewish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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: DSCAML1
Protein: p.Asp714=
Coding: c.2142C>T
MANE Select: NM_020693
dbSNP: rs139385882
Type: single nucleotide variant
Location: chr11:117504964 (GRCh38)
Gene constraint: LOEUF 0.253 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 69.92 · 1 PDB
Residue 714: the ig-like c2-type 8 domain

Full DSCAML1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

DSCAML1 p.Asp714Gly Uncertain significance ⚠ same residue
DSCAML1 c.-101C>T Uncertain significance ★★ same type
DSCAML1 c.-17T>C Uncertain significance ★★ same type
DSCAML1 c.-23G>A Uncertain significance ★★ same type
DSCAML1 c.-44C>T Uncertain significance ★★ same type
DSCAML1 c.-51G>T Uncertain significance ★★ same type
DSCAML1 c.-57G>A Uncertain significance ★★ same type
DSCAML1 c.-87G>A 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/dscaml1-p-asp714 (accessed [today's date]).

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