# NM_001765.3(CD1C):c.899T>C (p.Phe300Ser)

https://sugi.bio/variant/cd1c-p-phe300ser

## Summary

**CD1C p.Phe300Ser (c.899T>C)** is classified **Benign** in CD1C (ClinVar, Multiple submitters, 2 submitters; last evaluated 2018-07-27). AlphaMissense: likely benign (0.0872); Common (popmax 7.81%, eas) — too common for a highly-penetrant pathogenic allele.

**At a glance:** Benign · review: Multiple submitters · rsID rs3138105 · 2 submitters · AlphaMissense likely benign · common (popmax 7.81%, eas) — too common for a highly-penetrant pathogenic allele

## For patients & families {#patients}

This is a change in the CD1C gene that is classified as benign — not considered disease-causing, submitted by 2 submitters.

*Reference information, not medical advice, and not a prediction for any individual. A genetic counselor or clinician can interpret what it means for you and your family.*

**Support & next steps:** [Find a genetic counselor (NSGC)](https://findageneticcounselor.nsgc.org/).

## Identity {#identity}

| Field | Value |
| --- | --- |
| Gene | [CD1C](https://sugi.bio/atlas/gene/CD1C/) |
| Protein change (HGVS p.) | p.Phe300Ser |
| Coding change (HGVS c.) | c.899T>C |
| MANE Select transcript | [NM_001764](https://www.ncbi.nlm.nih.gov/nuccore/NM_001764) (variant reported on NM_001765) |
| dbSNP | [rs3138105](https://www.ncbi.nlm.nih.gov/snp/rs3138105/) |
| Variant type | single nucleotide variant |
| Location | chr1:158293221-158293221 (GRCh38) |
| ClinVar | [VCV773640](https://www.ncbi.nlm.nih.gov/clinvar/variation/773640/) |

**All HGVS expressions:** `NC_000001.10:g.158263011T>C`, `NC_000001.11:g.158293221T>C`, `NM_001765.3:c.899T>C`

## Computational & population evidence {#evidence}

**Concordance:** Evidence sources **disagree** — common (popmax 7.81%, eas) — too common for a highly-penetrant pathogenic allele.

- AlphaMissense **likely benign** (0.0872)
- REVEL 0.022 (moderately benign-leaning) — agrees with AlphaMissense
- SaProt LLR -5.373 (tolerated) — agrees with AlphaMissense
- → **In-silico consensus:** AlphaMissense, REVEL and SaProt all call this tolerated
- Conservation: phyloP -20, GERP -3.31 — fast-evolving / accelerated position
- CADD: **PHRED 0.631**. No single ClinGen-calibrated threshold exists and the expert panels that use CADD disagree — GUCY2D/AIPL1 require ≥ 20.0 for an untranslated-region variant, ABCA4 ≥ 28.1 for a synonymous or indel variant, the Pulmonary Hypertension panel imports Pejaver 2022's missense-calibrated numbers, and the Antibody Deficiencies panel declines CADD entirely for PIK3CD. CADD v1.7 also incorporates Zoonomia phyloP, so it partly re-expresses the conservation above. *Descriptive; no threshold applied.*
- Regional missense constraint: **o/e 1.06** across the covering region of the MANE Select transcript (158,290,065–158,293,473), spanning 3,408 bp. Chi-square p 0.27. Describes the region, not this allele; gnomAD v4.1.1's own constrained determination. *Descriptive; no ACMG code applied.*
- SpliceAI: **not looked up on this page** — it was served without the gene's SpliceAI index, so no lookup was made. This is a gap in this page, not in the data, and says nothing about whether a splicing effect is predicted.
- Population frequency (gnomAD v4.1): grpmax **7.81%** (eas) · FAF95 7.59% · FAF99 7.5% · 3,502/44,856 in the highest group · 4,312/1,613,520 alleles overall — common (popmax 7.81%, eas) — too common for a highly-penetrant pathogenic allele.

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| East Asian (grpmax) | 7.81% | 13 |
| Remaining individuals (not grpmax-eligible) | 0.844% | 119 |
| South Asian | 0.228% | 438 |
| Admixed American | 0.0333% | 3,001 |
| African / African-American | 0.028% | 3,573 |
| Middle Eastern | 0.0165% | 6,058 |
| European (non-Finnish) | 0.0028% | 35,743 |

*Computational predictors are not independent (ClinGen Variant Classification guidance): AlphaMissense (Cheng et al. 2023) carries the ACMG weight for missense and conservation (phyloP/GERP/phastCons) for non-missense; REVEL (Pejaver-2022 calibrated strength bands) and SaProt (Su et al. 2023, structure-aware, ClinVar-independent protein language model, raw LLR) are shown as orthogonal agreement signals, not additive. For frequency, the gnomAD v4.1 grpmax filtering allele frequency (FAF95) is ClinGen's designated BA1/BS1 input (gnomAD v4 guidance v3.0, June 2025); BA1/BS1 thresholds are disease-specific, not a blanket 5%. Predictions, not a clinical determination.*

## Clinical significance {#significance}

**Benign** — review status Multiple submitters *(criteria provided, multiple submitters, no conflicts)*, last evaluated 2018-07-27.

**Submitter consensus:** unanimous (2/2 Benign).

**Submission history:** 2 submissions (2018); classifications have been stable.

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Labcorp Genetics (formerly Invitae), Labcorp | Benign | criteria provided, single submitter | clinical testing | 2018-07-27 |
| Breakthrough Genomics, Breakthrough Genomics | Benign | criteria provided, single submitter | not provided |  |

**Reported phenotype names (ClinVar):** not provided, none provided, RECLASSIFIED - ADRA2C POLYMORPHISM, RECLASSIFIED - ADRB1 POLYMORPHISM.

### Data sources & attribution {#sources}

ClinVar (NCBI — public domain, built 2026-10-14); gnomAD v4.1 (Broad Institute, built 2026-10-06); AlphaMissense (Cheng et al. 2023, © Google DeepMind — CC BY 4.0, built 2026-01-27); REVEL (Ioannidis et al. 2016 — ODbL, built 2026-07-13); SaProt (Su et al. 2023 — MIT, built 2026-07-14); SpliceAI (Illumina — free for non-commercial use, built 2026-10-13); CADD (Rentzsch et al. 2019, University of Washington — free for non-commercial use, built 2026-10-10); Conservation (phyloP/phastCons/GERP) (UCSC hg38 470-way mammal (Hiller Lab) + Ensembl Compara, built 2026-07-12); gnomAD Non-coding Constraint (Gnocchi) (Chen et al. 2024, Broad Institute — CC0, built 2026-10-11); gnomAD Regional Missense Constraint (Broad Institute — CC0, built 2026-10-13); Pangolin (Zeng & Li 2022 — CC BY 4.0, built 2026-10-11); Repeat regions (UCSC — RepeatMasker, TRF, segmental duplications, built 2026-10-11); ClinGen (ClinGen, built 2026-09-22); UniProt (CC BY 4.0); Reactome / GO (CC BY 4.0, built 2026-09-23); MaveDB (per-record license, built 2026-10-11); CIViC (CC0, built 2026-09-22); Orphanet (Orphanet, built 2026-06-12)

*Primary record: NCBI ClinVar (variation 773640). Classifications reflect these databases as of the page's build date and may change. Free reference use — not medical advice; consult the primary submitters and a clinician.*